As the world's largest developing country, and as the home to many of the world's factories, China plays a crucial role in the sustainable development of the world economy regarding environmental protection, energy conservation, and emission reduction issues. Based on the data from 2003-2015, this paper examined the green total factor productivity and the technological progress in the Chinese manufacturing industry. A slack-based measure (SBM) Malmquist productivity index was used to measure the bias of technological change (BTC), input-biased technological change (IBTC), and output-biased technological change (OBTC) by decomposing the technological progress. It also investigated the mechanism of environmental regulation, property right structure, enterprise-scale, energy consumption structure, and other factors on China's technological progress bias. The empirical results showed the following: (1) there was a bias of technological progress in the Chinese manufacturing industry during the research period; (2) although China's manufacturing industry's output tended to become greener, it was still characterized by a preference for overall CO2 output; and (3) the impact of environmental regulations on the Chinese manufacturing industry's technological progress had a significant threshold effect. The flexible control of environmental regulatory strength will benefit the Chinese manufacturing industry's technological development. (4) R&D investment, export delivery value, and structure of energy consumption significantly contributed to promoting technological progress. This study provides further insight into the sustainable development of China's manufacturing sector to promote green-biased technological progress and to achieve the dual goal of environmental protection and healthy economic growth.