The invention discloses a power quality comprehensive evaluation method and system. The existing power quality comprehensive evaluation system has the disadvantage of poor practicability, and is even just a kind of furnishings in most cases, which makes it impossible to transform a power grid and improve the power quality level of the power grid in a targeted manner through power quality comprehensive evaluation results. The method provided by the technical scheme of the invention comprises the steps that different algorithms are scripted to form a script file; the script file is stored: the determined script file is edited and stored in a database; the script file is invoked, and specifically the corresponding script file is called from the database according to the selected algorithm to realize comprehensive power quality assessment and generate a comprehensive evaluation result; and follow-up processing of the power quality comprehensive evaluation result is carried out. According to the invention, the method and system support a plurality of evaluation algorithms at the same time, and support the comprehensive evaluation function including a steady-state index and a transient index, and can quickly adjust the algorithms according to actual needs.