Environmental pollution becomes one of the main barriers for high-quality development of agriculture while China’s agricultural production continues to grow. Taking the emission quantity of agricultural water pollutants (total nitrogen and total phosphorus) as non-expected output, based on the nonparametric directional distance function model, this paper measures and decomposes the growth index of agricultural green total factor productivity of China’s agriculture during 1999-2018 and further analyzes the output bias of technology progress and its influence factors. The results show that the green total factor productivity of China’s agriculture continues to grow, and the output biased technology progress is the important source of agricultural green TFP growth, China’s agricultural technology progress has obvious output bias, is totally green output biased(bias of pollutants emission reduction), shows the fluctuated rise of the number of the provinces that technology progress reduces the emission of total nitrogen and total phosphorus and displays the rise of all biased extent of technology progress green output but has spatio-temporal difference. The promotion of rural residents income level, agricultural human capital level, the ratio of grain planting area, urban-rural income gap, and agricultural policy support degree is conducive to the improvement of the biased extent of the green output of agricultural technology, however, the increase of urbanization level and agricultural fertilizers utilizing amount can prevent the rise of the biased extent of the green output of agricultural technology progress. The biased extent of the green output of agricultural technology progress should be continuously boosted by multi-measure such as agricultural support policies, environment regulation, green technology supply, agricultural producer development and so on so as to realize the sustainable development of agriculture and villages.