Microplastics (MPs) in aquatic environments has been observed globally. However, the ecological risks of MP pollution in riverhead prior to highly urbanized region remain poorly understood. This study investigated MP pollution related to microbiome in sediments, and ecological risks of MPs in riverhead prior to urbanized area over 291 km of Minjiang River (MJR) in Qinghai-Tibetan Plateau (QTP). MPs in river water and sediments were averagely 245±128 items/L and 124±67 items/kg, respectively, over the investigated river range. The MP distribution indicated that MP abundance is low in headwater section and elevated in middle section and down section with increase of urbanized area. The MPs were found mainly in film, fragments, and fiber morphotypes, with size < 500 μm in both river water and sediments. The polymers of MPs were contributed by polyethylene (PE), polypropylene (PP), polyethylene terephthalate (PET), polyvinyl chloride (PVC), and polycarbonate (PC) at 41.7 %, 22.7 %, 17.9 %, 1.8 %, and 1.2 % in river water, and 32.6 %, 15.0 %, 29.3 %, 3.1 %, and 0.8 % in sediments, respectively. Microbiome analyses of sediments revealed that the majority of microorganisms were aerobic bacteria, which contained potential plastic-degrading bacterial genes. Ecological risk assessment indexes of pollution load, polymeric risk assessment and pollution risk indicated that MPs in MJR river water and sediments displayed noticeable pollution levels, i.e., river water exhibited medium to very high pollution risk levels, and sediments showed from low to very high pollution risk levels in riverhead. Monte Carlo simulation revealed that PVC and PC MPs were considered as priority control pollutants although they were not the most abundant polymers identified due to their intrinsic chemical toxicity. Compared with risk levels of global rivers, the results indicate prominent ecological risks caused by MPs in MJR riverhead areas, and thus raise a warning sign.