Supported by the data of the pig breeding industry development and the basic technical and economic parameters of pollution production and discharge, by using SFA-Malmquist and other methods, the efficiency of waste resource utilization, environmental total factor productivity and other indexes have been defined and the utilization efficiency and trend of pig breeding waste in China from 2006 to 2017 have been analyzed. The research shows that China’s pig breeding industry is still a “capital investment” industry; the efficient utilization of waste resources and appropriate large-scale breeding are the key to the green growth of pig breeding economy. Under the constraints of environmental protection, the growth of environmental total factor productivity of the pig breeding has slowed down, and its growth is characterized by scale heterogeneity, time-variation and regional differences. The main driving factors of environmental total factor productivity are different on different scales. Technical efficiency is inversely related to technological progress. Medium-scale breeding has growth potential while the growth advantage of large-scale breeding declines significantly. The green development of China’s pig breeding industry must take into account the utilization efficiency of waste resources and the efficiency of breeding technology, and meanwhile pay attention to the advantages of different scales of breeding in different areas.