The performance of the structural monitoring system (SMS) is the key of structural safety assessment. Aiming at the difficulties of evaluation for in-service SMS, an online performance evaluation method based on data series feature analysis was proposed. In this method, the reference system was used to establish the dynamic comparison benchmark of the measured data, and the performance evaluation model was established by analyzing the structure characteristics of the matched data series under the natural excitation condition. A method based on character representation was proposed to solve the matching problem of data series of different shapes and scales. The field tests show that this method has the adaptability of multi-scale and large-range data series matching, and the calculation deviation of the proposed evaluation indexes for different samples is less than ±1%, so it has the practicability of long-term quantitative evaluation of the structural monitoring systems.