Taking listed companies as sample and using three stage DEA-Malmquist index model which considers environmental factors, this paper makes empirical analysis on the real growth features and industry differences of total factor productivity in China’s bio-agriculture. The results show that rapid expansion of macro economy, increase of government subsidies and excessive concentration of ownership structure, are not conducive to improve total factor productivity; growth of total factor productivity is more significant which driven mainly by technical efficiency and technical level is backward after eliminating influence of environmental variables and random errors; sample differences of total factor productivity growth is obvious, development of various sub-sectors is relatively balanced, but development of internal sub-sector is uneven. Therefore, government should optimize external environment, promote technological innovation, and strengthen classification guidance in order to improve total factor productivity of bio-agriculture more effectively.