[Objective] This study focuses on water content as the key controlling factor to clarify the time-dependent patterns of thixotropic strength recovery of Zhanjiang Formation structural clay under different initial water contents. The microscopic mechanism is interpreted through three pathways: pore structure evolution, particle reorganization, and water action. The findings are expected to provide experimental evidence and theoretical support for predicting strength recovery and evaluating the stability of thixotropic clay foundations. [Methods] Remolded Zhanjiang Formation structural clay specimens were prepared and subjected to a 150-day thixotropy test. Specimens at different thixotropic durations were investigated using macroscopic and microscopic tests. For macromechanical testing, unconfined compressive strength (UCS) tests were conducted on cylindrical specimens. Direct shear tests were conducted on ring-knife specimens to obtain UCS, cohesion (c), and internal friction angle (φ), which were used to evaluate thixotropic evolution. A thixotropic strength ratio was defined as A_t = m_t/m₀, and two indicators—A_t(q) (based on UCS) and A_t(τ) (based on cohesion)—were used to compare recovery characteristics among different strength parameters. For microstructure, fabric evolution was observed using an SEM. Pore parameters, including porosity (M) and abundance (C), were extracted to quantitatively analyze pore structure evolution. Particle parameters, namely probability entropy (H) and distribution fractal dimension (D), were used to quantitatively characterize particle orientation/orderliness and aggregation degree, respectively. [Results] (1) Stage-dependent recovery: Both UCS and cohesion (c) increased with thixotropic duration and showed two stages: a rapid and significant recovery phase during 0-30 d, followed by a slower, stable phase during 30-150 d. The increment during 100-150 d was small, indicating near-stabilization, after which the test was terminated. (2) Dual effect of water content: At the same thixotropic duration, UCS generally decreased with increasing water content, reflecting weakened particle contacts and bonding and thus reduced instantaneous strength. However, higher water content resulted in a faster strength recovery rate, especially at early stage, indicating that water promoted the kinetics of self-adaptive structural adjustment during thixotropic process. (3) Indicator-dependent differences: Cohesion exhibited a higher thixotropic strength ratio and faster recovery within 1 d, suggesting that shearing promoted directional particle alignment and optimized the friction-bonding interface, making c more sensitive to structural rebuilding than UCS. (4) Coordinated micro-parameter evolution: As thixotropic duration increased, M and c decreased continuously. Pores shifted from “large and numerous inter-aggregate pores” to “small and fewer intra-aggregate pores”, while the overall pore shapes remained mainly quasi-equant but became denser. Additionally, H and D decreased synchronously, indicating enhanced particle orientation/orderliness and increased aggregation. These changes were most significant within the first 30 d, consistent with the rapid macroscopic recovery stage. SEM observations revealed a transition from an “open flocculated-dispersed” fabric to a “closed flocculated-aggregated” fabric. Pores between and within aggregates decreased, while particle contacts and continuity of force-transfer paths improved, thereby supporting strength recovery. [Conclusion] The thixotropic strength recovery of Zhanjiang Formation structural clay exhibits distinct time-stage characteristics and strong sensitivity to water content. Recovery generally progresses through a rapid phase (0-30 d) and a stable phase (30-150 d). Higher water content reduces the strength level but significantly accelerates the strength recovery rate. Cohesion exhibits a higher thixotropic strength ratio than UCS because shear-induced particle orientation facilitates more effective structural reconstruction. Microscopically, synchronous decreases in M/C and H/D indicate pore reduction, particle ordering, and aggregation densification. Water enhances particle activity by altering relative particle positions and expanding migration pathways, thereby accelerating self-adaptive adjustment and strength recovery during thixotropic process. Innovations included: (1) parallel comparison of UCS and rapid direct shear parameters within a single thixotropic framework, revealing the cohesion recovery advantage caused by shear-induced particle orientation; (2) linking the macroscopic two-stage recovery pattern with the coordinated evolution of M, c, H, and D, forming an evidence chain of “structural rearrangement—aggregation densification—strength recovery”; and (3) demonstrating that higher water content, while reducing instantaneous strength, accelerates recovery by enhancing particle mobility/activity.