The invention relates to a comprehensive evaluation method for operation monitoring of a comprehensive atmospheric observing system. The comprehensive evaluation method for the operation monitoring of the comprehensive atmospheric observing system comprises the following steps: building a comprehensive analysis and evaluation model in a comprehensive atmospheric observing system operation monitoring platform, wherein the comprehensive analysis and evaluation model comprises the following evaluation sub-modules: a detection system serviceability evaluation sub-module, an atmospheric equipment maintainability evaluation sub-module, an equipment supply supportability evaluation sub-module, a detection service work evaluation sub-module, a station network layout comprehensive evaluation sub-module and a detection system economic benefit evaluation sub-module; determining an evaluation range of each evaluation sub-module, evaluation indexes of evaluation programs in an evaluation range and computing methods of the evaluation indexes; collecting data required by evaluation, obtaining evaluation results according to the computing methods, and forming a graph of a preset format with a function of reflecting the evaluation results according to a preset method to output. The comprehensive evaluation method for the operation monitoring of the comprehensive atmospheric observing system can effectively support the smooth operation of an atmospheric detection support service.