Benthic metabolism is an essential process which plays a critical role in the carbon and nutrient cycles and in the transfer of material and energy in stream ecosystems. Benthic algae are one of principal primary producers in stream food webs that converts dissolved inorganic carbon to organic matter, and algae are more palatable basal resources for aquatic consumers due to its higher unsaturated fatty acid content than terrestrial carbon. Despite the importance of algae, few studies have investigated how the benthic metabolism is influenced by distal factors, such as upland land use and landscape configuration, and proximal factors, such as stream temperature, nutrient availability, and light availability at various spatial scales. Here, we measured the benthic metabolism and proximal factors at the outlet of 14 selected sub-catchments in a subtropical river. Land use and landscape metrics at the catchment, riparian, and reach scales were processed as distal factors. Using stepwise regression models, we found that the proximal factors, such as water temperature (WT) and total phosphorus (TP), significantly increased primary production, and that nitrate-nitrogen (NO3--N), pH, and electrical conductivity (EC) decreased gross primary production (GPP). Also, TP was positively correlated with respiration (R) while NO3--N negatively impacted R. Structural equation modeling demonstrated that the patch cohesion index negatively affected GPP by restraining WT and TP at the catchment scale while the increased shape index elevated the WT and TP to promote GPP. Our results suggested that stream metabolism is vulnerable to anthropogenic disturbances, such as upland land use and landscape patterns. Thus, land use planning and administration, particularly at catchment scale, should consider how to minimize the influence of human activities on ecosystem function in streams.