The dual problems of the public crisis from the global epidemic and the deterioration of the ecological environment constrain the economic development in the Yellow River Basin. To promote the sustainable and balanced development in the Yellow River Basin, this paper takes public health, ecological environment, and economic development, as a whole, to study the coordinated development of the Yellow River Basin. Based on coupling coordinated theory, we use the SMI-P method to evaluate the coordinated development index of public health, the ecological environment, and economic development in the Yellow River Basin. Moreover, we use the coordinated regulation and obstacle factor diagnosis to identify the main influencing factors and design regulation methods to optimize the coordinated development index. The results found that (1), during the research period, there is spatiotemporal heterogeneity in the coordinated development level in the Yellow River Basin. From 2009 to 2019, the overall development index increased steadily, while the regional disparity in the coordinated development level was obvious. (2) The ecological environment indicators contribute more to the relevance and obstacle factors, such as the average concentration of fine particulate matter, per capita arable land area, afforestation area, etc. (3) After regulating the overall development level of the Yellow River Basin, we prove that Path 4, which comprehensively considers the relevance and obstacle factors, performs better.