Carrying the comprehensive decision-making about the harmonious development between the regional economy and environment into execution is significant to improve the economic and environment quality in China. Based on the running mechanism of the harmonious development between the regional economy and environment, this paper brings forward the main approaches to the comprehensive decision-making on the harmonious development between the regional economy and environment: Establish and consummate the comprehensive decision-making system about the harmonious development between the economy and environment; Forbid strictly the moving of the contaminations during the updating industry structure; Insure the three economy core areas to be the ones of the harmonious development between the economy and environment; The emphatically exploited axis areas should be the ones whose environments are emphatically protected; All kinds of economic and technological development areas should beconstructed as the demonstrating areas of the harmonious development areas between the economy and environment.