The Cenozoic Himalayan granites are widely accepted as the anatectic products of crustal rocks. However, previous geochemical studies on their petrogenesis are mainly based on whole-rock analyses. Here we conducted a detailed petrographic, trace elemental and Sr isotopic investigations of apatite from the Middle Eocene (44–40 Ma) two-mica granites and subvolcanic porphyritic leucogranites of the Yardoi-Lhunze complex from the Tethyan Himalayan Sequence in the southeast Tibet, with the aim to constrain their magma sources and petrogenetic processes. The results show that apatites from the Quedang and Dala two-mica granites are characterized by euhedral to subhedral crystal shape, and have a wide range of initial 87Sr/86Sr ratios (0.7016–1.0088). They show significant negative Eu anomaly and varied concentrations of Sr and Y, indicating they are typical magmatic apatites. Apatites from the Qiaga porphyritic leucogranites can be divided into two groups based on Eu anomaly. Group-I apatites with positive Eu anomaly mainly display euhedral to subhedral crystal shape but with alteration rim, suggesting from the influence of hydrothermal fluids. Group-II apatites with negative Eu anomaly also have euhedral to subhedral crystal shape but they exhibit patchy or oscillatory zones, consistent with a magmatic origin. However, both group-I and II apatites have comparable initial 87Sr/86Sr ratios, 0.7198–0.9966 and 0.7174–0.9999, respectively. Previous studies based on whole-rock petrology and geochemistry have suggested that the Quedang and Dala two-mica granites and the Qiaga porphyritic leucogranites represent cumulates and fractionated melt-rich magmas, respectively. This is evidenced by systematic variations between Sr, Y, (La/Sm)N and Eu/Eu* in magmatic apatites from Quedang and Dala, consistent with the fractionation crystallization of plagioclase and monazite.Apatite has a wide range of initial 87Sr/86Sr ratios (0.7016–1.0088), far exceeding the range of whole-rock records (0.7011–0.7204). Notably, most of the analyzed apatites show lower range of initial 87Sr/86Sr ratios consistent with locally exposed amphibolites (0.7109–0.7332). The remaining small portion of apatites have initial 87Sr/86Sr ratios falling within the data range of the locally exposed metapelites (0.8517–0.9527). Therefore, the investigated granites have mixed magma sources dominated by amphibolites with subordinate metapelites. This can be inferred by apatite Sr isotopes alone, but not by whole-rock Sr isotopes alone. Our investigations highlight that in-situ geochemistry of apatite can provide a powerful means to unravel the mixed magma sources and complicated magmatic processes for granites.