Resource-saving agriculture and environment-friendly agriculture is a complex organism involving production, economy, society and ecology. Its development process is influenced by various factors, such as producers, nature, society, etc, and so is agricultural production efficiency. In order to overcome the measurement error of traditional data envelopment analysis caused by ignoring random factors, this paper employed the three-stage data envelopment analysis model to remove environmental factors and random effects. On the basis of this model, it estimated the resource-saving agriculture and environment-friendly agriculture comprehensive production efficiency of 31 provinces and cities in China, and brought forth corresponding policy proposals to promote agricultural development.