As the main primary producer in stream ecosystems, periphyton is the fundamental of stream ecosystems and plays an essential role in maintaining stream biodiversity. The central Hengduan Mountains is one of the famous global biodiversity hotspots. However, for stream biodiversity conservations, the fundamental information about the spatial pattern of stream periphyton and the determining factors in this region remains largely unknown. To fill this gap, we investigated the spatial pattern of periphyton biomass (measured by chlorophyll a) in four typical streams in the central Hengduan Mountains and analyzed the driving factors, with the perspective of watershed land use and instream water quality. The results of our study found that farmland area, instream dissolved silicate (DSi), and water temperature (WT) had significant negative relationships with the stream periphyton biomass in the central Hengduan Mountains. However, the dissolved inorganic phosphorus (DIP) and dissolved inorganic nitrogen (DIN) had non-significant effects on the periphyton biomass in our study. Further analysis showed that the correlation between the ratio of farmland in the catchment and the DSi is non-significant (r = 0.028, P = 0.698), suggesting that the changes in farmland area will not affect the concentration of dissolved silicate in the stream. This reveals that the stream periphyton biomass was co-determined by the watershed farmland area and instream DSi and WT, but not nitrogen or phosphorus. These results highlight the importance of farmland management and instream DSi for stream ecosystems in the central Hengduan Mountains. Our study investigated the spatial pattern of the stream primary producer in the central Hengduan Mountains region and identified the main determining factors, which could improve our understanding of the high mountain stream ecosystems.