Based on Public Expenditure Model and cost function theory,this paper first constructs agricultural cost modeling under the optimized condition,then this paper treats inputs of labor,fixed capital and fertilizers as the component of agricultural cost,and uses Quantile Regression to analyze the effect of irrigation facility and substandard highway on China’s agricultural production cost at provincial level from 1995 to 2011. The result indicates that construction of irrigation facility and substandard highway has the positive effect on China’s agricultural production cost and elasticity coefficient of agricultural production cost is also positive.With the increase of agricultural production cost,the effect of irrigation facility is increasing,but the effect of substandard highway is first increasing and then decreasing.