Present control index systems for soil deformation is insufficiently targeted, scientific, and applicable. In view of this, we present a comprehensive method of determining the deformation control index for the tunnel project of Xiamen metro line in weathered granite stratum as an example. The method introduces the spatial variation of soil parameters based on statistical analysis of field monitoring data and stochastic reliability analysis. Results demonstrate that in the typical weathered granite stratum in Xiamen, the statistical mean value of the maximum surface settlement caused by shield tunneling is -13.5 mm, and the 95% quantiles of maximum surface settlement is -32.42 mm. According to the stochastic reliability analysis, the maximum surface settlement is in the form of standard normal or lognormal distribution, and the 95% quantiles of maximum surface settlement obtained by stochastic calculation is - 35.43 mm. From the point of view of safety, we suggest to take -35.0 mm as the control value of surface settlement during the twin shield tunneling in Xiamen typical weathered granite stratum.