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.