Traditional production functions rarely consider the role of natural resources in crop production and the damage to the environment caused by use of fertilizers and pesticides. This paper introduces green, blue, and grey water footprints representing natural water resources, irrigation water resources and the impact of crop production on the environment, and assesses crop production eco-efficiency and its influential factors in Shaanxi Province through the stochastic frontier approach. The results showed that:1) From 1985 to 2018, the crop production water footprint of Shaanxi Province presented an upward trend and the water intensity per unit area was continuously enhanced. The water footprints per unit area and the proportions of blue, green, and gray water were related to climate, planting structure, irrigation conditions and crop production pollution. 2) During the research period, the eco-efficiency of crop production in Shaanxi Province demonstrated a trend of decreasing first and then increasing, taking 2003 as a cut-off point. The ecological efficiency of crop production in Shaanxi Province fluctuates in "U" shape, which corresponds to the changes of the government's policy of protecting cultivated land resources and agricultural pollution control. 3) Low eco-efficiency regions are concentrated in agricultural areas with backward production mode and industrial areas with poor agricultural conditions. The main reasons for the low eco-efficiency of crop production lie in the poor quality of agricultural arable land, scarce irrigation water resources, inefficient irrigation water, fertilizer and pesticide application, and backward mode of production. 4) During the study period, crop production in Shaanxi Province experienced two stages, from increasing returns to scale to decreasing returns to scale, basically corresponding to the change of cultivated land area. In the short term, adjusting the planting structure and controlling fertilizers and pesticides applications are effective ways to improve the eco-efficiency of crop production. However, the fundamental path is the upgrading of agricultural industry and technological innovation.