Watershed field town development along the river, an important mode of urban development in mountainous areas in southwest China, has brought a series of environmental problems for river and impacted the riverine biogeochemical process. However, the effect of field towns development on the spatial-temporal pattern of riverine greenhouse gas emissions are not clear. In this study, the Heishuitan river, whose watershed is undergoing rapid town development, was selected to investigate greenhouse gas concentration and diffusion fluxes in the surface water of main stream and its tributaries from September, 2014 to June, 2015. The results showed that annual average of partial pressure of carbon dioxide (pCO₂), methane (CH₄), and nitrous oxide (N₂O) concentrations in the main stream and tributaries were all oversaturated, which indicated that Heishuitan river was the net emission source of atmospheric greenhouse gases. The concentrations of carbon, nitrogen, phosphorus, and chlorophyll a in water increased to different extents before and after it flowed through different towns. This suggests obvious accumulation of pollutants due to the pattern of town distribution in Heishuitan basin. Meanwhile, CO₂, CH₄, and N₂O concentrations and diffusion fluxes from Heishuitan river also showed significant increases before and after different towns with average increase ratio of diffusion fluxes of 25.88%, 55.22%, and 99.64%, respectively. pCO₂ and N₂O concentration were found higher in autumn than in other seasons, while the concentrations and diffusion fluxes of CH₄ was the highest in spring, followed by autumn, the lowest in summer and winter. The seasonal pattern was co-regulated by both water temperature and precipitation pattern. Correlation analysis showed that pCO₂ was closely related to water temperature and pH, while CH₄ and N₂O concentrations were positively correlated with the biological elements such as carbon, nitrogen, and phosphorus, reflecting that the concentration of CH₄ and N₂O in water body of biological elements input was extremely sensitive. The pollution load increase due to the watershed town development may have a significant excitation effect on the CH₄ and N₂O emission from rivers. In this study, the distribution of the beaded field towns along the river in mountainous areas would have cumulative impacts on the river water biogenic element and other physical and chemical properties, thus changing the spatial and temporal pattern of the greenhouse gas generation and emission.