Understanding the responses of nitrogen and phosphorus outputs to precipitation and temperature is vital for agricultural nonpoint source pollution under climate change. Nitrogen and phosphorus pollution loss characteristics of a typical low-temperature agricultural region in the Sanjiang Plain of China was simulated in this study using the SWAT model based on meteorological factors from 1975 to 2014. The average daily temperature increased with a slight trend of 0.132 ℃·10a~(-1), while precipitation began to decline since the 1980s, with a total reduction less than 140 mm and large differences in annual yield(11.60~415.50 mm). N and P outputs were positively correlated with precipitation. The N and P yields of high flow years were 1.5- and 2.5-fold, respectively, higher than that of low flow years, and the sensitivity of variation decreased with the increase of precipitation. In contrast, N and P outputs were negatively correlated with temperature(0.937 kg·hm~(-2)·℃~(-1), 0.161 kg·hm~(-2)·℃~(-1)). Yearly data showed an increase in N and P outputs under climate change in the study area, which revealed that anthropic factors might play an important role. Therefore, for studies on the response of non-point nitrogen and phosphorus output to future climate change, it is necessary to consider both impact of nature and humans.