As essential parts of the unique ecosystem of Tibetan Plateau (TP), the sizes and associated physical properties of alpine lakes have long been investigated. However, little is known about one of the most critical biogeochemical properties, i.e. the Chlorophyll-a (Chl-a) concentrations. Here, for the first time, we presented a comprehensive investigation of the temporal–spatial variations in Chl-a in 82 lakes (>50 km²) across the entire TP region, based on MODIS observations in the period of 2003–2017. The results showed that the 82 lakes exhibited an average long-term mean Chl-a of 3.3 ± 4.3 mg m⁻³, with high Chl-a lakes concentrated in the eastern and southern inner TP basin and northeastern parts of the TP. An interannual trend analysis revealed that lakes exhibiting (significantly) decreasing Chl-a trends and (significantly) increasing Chl-a trends were comparable in numbers but differed in distribution patterns. A correlation analysis indicated that at least 70% of the interannual variability in Chl-a values of lakes was significantly correlated with one of the four environmental factors (wind speed, ice cover duration, lake water surface temperature and surface runoff) and lake size. In addition, glacier meltwater tended to reduce lake Chl-a while salinity levels showed minor influences.