Continuously promoting of agricultural total factor productivity (TFP) is inevitable requirement for agricultural modernization at new era. Based on stochastic frontier production function, this paper constructs a transcendental logarithmic production function model to measure agricultural TFP of 31 provinces and municipalities during 2000-2014, and uses dynamic SAR model to analyze spatial spillover effect of agricultural TFP. The results show that the overall agricultural TFP has a certain degree of growth, but the growth tends to decline in recent years, that the dynamic effect plays a significant role in agricultural TFP, showing a strong inertia of development, that agricultural TFP has significantly positive spatial spillover effect, that adjacent regions’ agricultural TFP will promote each other, that the main input of agricultural production not only directly affects the agricultural TFP growth itself significantly, but also affects the neighborhood's indirectly. Therefore, some countermeasures are put forward, including strengthening agricultural input, regional cooperation, policy support etc., to promote the sustained and rapid growth of agricultural TFP by sufficiently taking advantage of the spatial spillover effect and dynamic effect of agricultural TFP.