High-quality industrial development is an important part of the strategy of ecological protection and high quality development in the Yellow River Basin. In order to study the spatial differentiation of high-quality industrial development in the Yellow River Basin in the past decade, this paper uses EFTP (ecological total factor productivity) as the measurement standard, measures and analyzes the industrial development level of the main cities and urban agglomerations in the Yellow River Basin from 2006 to 2016 through super efficiency DEA and Malmquist index model, and finds that: the industrial development quality level of the Yellow River Basin is uneven, with the overall performance of East > West > Middle, In particular, the productivity of Shandong Peninsula urban agglomeration is much higher than other regions. The neighbor effect of industrial EFTP in different cities is significant, showing the characteristics of aggregation distribution. During the study period, the industrial EFTP in the Yellow River Basin increased at an average annual rate of 7.5%, the growth rate in the western region was faster, the late development advantage was fully reflected, and the growth in the eastern and central regions was slower. The central region has always been at a low level of development. It is urgent to adjust industrial development strategies and improve technical efficiency in order to promote the overall high-quality development of industry in the Yellow River Basin.