Manufacturing innovation efficiency is one of the important dimensions of high-quality economic development in Beijing-Tianjin-Hebei region. In this sense, this paper, via DEA-BCC model and Malmquist index, analyzes the innovation efficiency and its variations of the manufacturing industry in Beijing-Tianjin-Hebei region, ranging from 2016 to 2019. Accordingly, the panel Tobit model is employed to analyze the factors influencing the innovation efficiency of manufacturing industry. The results show that the innovation efficiency of manufacturing industry in this region is mainly manifested by the increasing scale reward and the overall low levels in terms of technology innovation, such as the total factors productivity (TFP), technology efficiency (TE), and scale efficiency (SE). In this regard, most industries are in a state of very low efficiency. Through the calculation of Gini coefficient, it is also found that there is a significant gap in the innovation efficiency of different industries, and the inequality between industries has become prominent and increasingly serious. Further calculation of Malmquist index demonstrates that the overall innovation efficiency in question tends to rise from 2016 to 2019; From the perspective of industry segmentation, the efficiency advantage of high-tech industry is more remarkable than that of low-tech industry, accordingly, the technology level has a positive effect on innovation efficiency; Finally, via the panel Tobit model, we find that some factors are positively correlated with manufacturing innovation efficiency, namely, government subsidies, main business income, marketization process, and direct foreign investment, thereby promoting the efficiency. It is also noted that financing constraints are negatively correlated with innovation efficiency, thus inhibiting the improvement of innovation efficiency.