Irrigation and water conservancy is an important part of agricultural infrastructure investment,which has important impact on agricultural economic growth and farmers’ income increase. This paper uses DEAMalmquist method to estimate the irrigation and water conservancy efficiency of 31 provinces based on the data from 2001 to 2015. Result shows that the efficiency of farmland water conservancy is different between those areas: the efficiency of northeast is higher than that of east China and central China. Such areas have more agricultural provinces. Irrigation and water conservancy efficiency does not completely match the regional economic development level mainly because of the nonlinear of irrigation and water conservancy efficiency and its influential factors. On the basis of provincial differences of water conservancy efficiency, the paper uses the estimating method of threshold panel estimation to checkout the threshold factors which have impact on the efficiency of farmland water conservancy. The results show that rural economic development level has a significant convergence threshold effect on water conservancy efficiency and mechanical power input has obvious threshold effect on the acceleration of water conservancy efficiency.