Based on the establishment of trans-logarithmic production function of agriculture which includes investment in farmland water conservancy, the stochastic frontier approach is used to calculate the total factor productivity of agriculture in 31 provinces(municipalities and autonomous regions)of China from 1996 to 2015. The spatial characteristics of the total factor productivity of agriculture and the influences of investment in farmland water conservancy are analyzed. The results show that the growth of the total factor productivity in China generally has an increasing trend. The horizontal and vertical analyses shows that the growth has regional property and regional agglomeration. The influences of investment in farmland water conservancy infrastructure on the total factor productivity of agriculture are positive, and they have weak spillover effect. Among them, the direct, indirect and total effects are 0. 2865, 0. 0574 and 0. 3439, respectively.