Agricultural machinery has been one of the most important sources of air pollution in China. It is very necessary to do more research on its emissions. This study aims to investigate the effects of burning different proportions of biodiesel in agricultural tractors at high altitudes on the emission characteristics of CO (carbon monoxide), HC (hydrocarbon), NOX (nitrogen oxides), and PN (particulate number) under the actual operating conditions. A series of tests were carried out on the blending B10 (10% by volume of soya bean methyl ester biodiesel + 90% by volume of diesel fuel), B20, B30, and diesel fuel (B0) in a National III emission standard agricultural tractor at an altitude of 2 200 m during rotary plowing (with the engine speed at 1 500 to 1 700 r/min and the engine power at 20 to 30 kW). OBD (board diagnostics) and PEMS (portable emission measurement system) were used to collect data on the tractor operating conditions and pollutants, respectively. The results showed that the biodiesel slightly reduced the fuel economy for the brake-specific fuel consumption (BSFC), which increased by 2.31%, 2.71%, and 2.04% for B10, B20, and B30, respectively, compared with B0. The emission factors were also obtained for the CO, HC, NO_X, and PN of agricultural tractors using engine power. Specifically, the CO, HC, and PN emission factors of agricultural tractors were reduced by 10.15%, 12.73%, and 32.10% for B10, B20, and B30, respectively, compared with B0 using biodiesel engine power; 13.22%, 26.45% and 30.58% for B0-based power; and 8.22%, 10.91% and 30.58% for B0-based power; and 8.22%, 10.91% and 30.58% for B30-based PN emission. B0 power-based PN emission factors were reduced by 8.22%, 10.91%, and 14.17%, respectively. The CO, HC, and PN emission factors increased with the increase in the percentage of biodiesel. Biodiesel slightly increased the NO_X emissions from agricultural tractors. The NO_X emission factor increased, as the proportion of biodiesel increased. The NO_X emission factors for B10, B20, and B30 increased by 1.60%, 2.78%, and 4.20%, respectively, compared with B0-based engine power. The power-based NO_X emission factors of all tested fuels in the plateau environment were more than three times higher than the recommended values of the Guideline. There was a great variation in the pollutant emission of the tractor during actual operation. A tradeoff was made on the fuel economy and the effect of biodiesel on NO_X emissions, in order to reduce the pollutant emissions from agricultural tractors during actual operation at high altitudes. Biodiesel can be expected to serve as an alternative fuel in small proportions for agricultural tractors. The CO, HC, and PN emissions can be reduced to avoid the use of fossil fuels. The finding can provide a strong reference to optimize the actual control of the pollutant emission of biodiesel combustion in agricultural tractors under high-altitude environments. The emission database of agricultural machinery can also be supplemented to reduce environmental pollution in high-altitude areas.