The invention relates to a comprehensive evaluation method for selection of favorable zones of medium-order coal bed gas reservoirs in small and medium-sized subsidence basins. The comprehensive evaluation method comprises the following steps: 1, evaluating the gas production capacity of a target coal seam; 2, evaluating the reservoir capacity of the target coal seam; 3, evaluating the storage condition of the target coal seam; 4, evaluating the permeability of the target coal seam; 5, defining coal bed methane accumulation main control factors of the target zone, predicting distribution characteristics of the main control factors by utilizing logging, earthquake and experiment analysis data of the research zone, superposing favorable zones of the main control factors, and comprehensivelyanalyzing and predicting favorable high-permeability enrichment zones. The method aims at the actual situation that the exploration degrees of a plurality of coal-bearing basins are different; according to the method, the parameters are reasonably classified, through comprehensive evaluation of the evaluation parameters, the coal bed methane reservoir area can be accurately and effectively judgedto the maximum extent, and the problems that according to an existing evaluation method, due to limitation of the evaluation parameters, evaluation is inaccurate, the selection target of coal bed methane is not clear, and manpower and material resources are wasted are solved.