Purpose: Alpine ecosystems in the Three River Headwaters Region (TRHR) are affected by phosphorus limitation, but it is still unclear how climate factors affect soil total phosphorus (TP) with the change of soil layers. Methods: In this study, we used data from 256 soil samples collected in 2019 to explore the direct and indirect effects of climate factors on soil TP in different soil layers. Results: Our findings suggested that within the top 80 cm, the average soil TP content was 0.47 g kg-1, and soil TP contents were 0.59 g kg-1, 0.48 g kg-1, and 0.41 g kg-1in the shrub, the meadow, and the steppe. The soil TP was higher in the shrub than in the meadow and the steppe. The soil TP content decreased gradually from southeast to northwest in all soil layers. With the increase of mean annual precipitation (MAP) and mean annual temperature (MAT), soil TP increased in all soil layers and vegetation types. With the increase of soil layers, the effects of climate factors on soil TP shifted from positive direct effects to positive indirect effects through vegetation and soil properties. It was worth noting that the effects of climate factors on soil TP may be more applicable to the meadow. Conclusions: Climate factors affect soil TP through divergent mechanisms in different soil layers. It should strengthen monitoring of soil TP under ongoing climate change to provide ideas for alleviating phosphorus limitation in the TRHR alpine ecosystems.