The invention relates to an online master station operation monitoring and evaluation method based on an index system. The method comprises the following steps: (1) master station system operation state indexes are classfied according to data features, and a multi-level index system is built; (2) an acquisition client complets classified acquisition and transmission on the index data; (3) an evaluation service end carries out analysis on index files, the index files are stored and put in storage, indexes are scored, a trend is evaluated, warning information is published, and an evaluation result report is provided; and (4) the evaluation result is comprehensively displayed via a man-machine interface. The method realizes dynamic master station system operation state monitoring, analysis, evaluation, online warning and comprehensive display, the problem that the master station system operation monitoring means is weak is solved, hidden dangers existing in the master station system can be found out in advance, master station system operation robustness is enhanced, the risk prevention ability of the master station system is enhanced, and decision basis is provided for improving, updating and optimizing the master station system.