Special engineering properties of loess often lead to hazards of highway culvert in the loess area. In order to address the problem of post-construction settlement of highway culvert caused by poor foundation in collapsible loess area, we treated the foundations of two highway culverts on collapsible loess area of the highway from Minhe to Xiaoxia in Qinghai province as a case study by replacing loess with lime-soil (hereinafter referred to as replacement method) and by filling lime-soil into boreholes for compaction (hereinafter referred to as compaction method), respectively, and monitored the settlements of the treated culverts for one year. Results revealed that the accumulative total settlements of culvert treated by the two methods were 25.0 mm and 18.2 mm, respectively. Both the methods could effectively eliminate the collapsibility deformation of highway culvert caused by water immersion and remarkably improve the bearing capacity of foundation. Foundation settlements became stable in a year after the foundation treatment. The compaction method is more efficient in eliminating deformation and improving bearing capacity than replacement method. The research result serves as a reference for the design and construction of highway culvert in collapsible loess area.