Microplastics (MPs) in freshwater have been extensively studied on a global scale. However, a deeper understanding is still required regarding the occurrence characteristics and ecological risks of MPs in protected area lakes(PAL). Here, the study investigated MPs pollution in PAL, outside protected areas lakes (OPAL), and ponds (OPAP) in the eastern Qinghai-Tibetan Plateau, and a comprehensive analysis was conducted comparing lakes or ponds from different income regions. The results showed that PAL has a single source of contamination, while OPAL and OPAP exhibited more diverse MP sources. The surface of all samples showed significant physicochemical changes like oxygen-containing functional groups and potential signs of biodegradation. Microbiome analysis identified potential plastic-degrading bacteria on MPs, which varied by polymer type. Ecological risk assessment revealed that OPAL and OPAP face higher ecological risks, particularly from polymers like PVC and PC, while PAL has low risk. However, we should also consider the environmental changes over the past 100 years of history in this region and emphasize the environmental health of PAL. Notably, MPs pollution is more severe in lower-middle-income regions, highlighting the urgent need for stricter controls.