China’s agricultural structure has undergone significant changes for the past four decades, mainly presenting as the fall of sown proportion of grain crops and the rise of vegetables, as has its energy consumption. Employing the panel data on 30 provinces during 1991–2016, this paper empirically explores the impact of agricultural structure changes (ASC) on the energy intensity of agricultural production (EIAP), direct energy intensity of agricultural production (DEIAP) and indirect energy intensity of agricultural production (IEIAP) in China. Besides, the regional heterogeneity of such impact is examined. The results show that: (1) ASC increases EIAP and IEIAP significantly, while ASC decreases DEIAP, which is explained by the structural effect and different planting modes of different crops; (2) the impact in the three administrative regions is similar to national situation, except the impact of ASC on DEIAP in the West Region, which is explained by regional differences of vegetable mechanization; (3) the result of the six vegetable production regions reveals greater regional heterogeneity, and this is attributed to the scale economy effect and the incremental effect of vegetable mechanization; and (4) fuel price, income, agricultural labor, old dependency ratio, and fiscal expenditure have different but significant impacts on EIAP, DEIAP, and IEIAP. Finally, some policy implications are given.