Increase in CO2 emissions induced by agricultural inputs in China since its socialist market economic reforms may hinder its sustainable economic development. More attention has been paid to changes in agricultural land use and overall land use benefit; however, relatively less attention has been paid to changes in CO2 emissions induced by agricultural inputs in China since the reforms. The carbon footprint (CF) variation for total agricultural production, the effects of different inputs on the total CF, and the changes in carbon intensity of the agricultural production system were analyzed using national level agrochemical and energy inputs data for the period 1991 to 2014. The total CF had a fluctuating upward trend, which was mainly affected by increases in nitrogen fertilizer input and energy consumption. The carbon intensity in production decreased, which indicated that the agricultural output value per unit of carbon cost gradually increased according to the market demands. However, the increase in agricultural output value per unit of carbon cost cannot outweigh the potential environmental risks induced by the increase in total carbon footprint per unit area of agricultural land. The improvements promoted by the related agricultural policies in China should aim to strike a balance between agricultural economy development and low carbon intensity in area.