The invention relates to a physiological signal quality evaluation method and system based on constrained estimation. The method comprises the following steps: receiving to-be-evaluated signal sections of a quasi-periodic physiological signal, performing pretreatment, waveform analysis identification and signal period segmentation to the signal sections, carrying out feature point detection to each cycle of signal section, and extracting preset physiological feature parameters of the physiological signal; for each signal section, combining the extracted physiological feature parameters to form feature vectors, performing constraint-based modeling according to transcendental knowledge of the physiological signal, and further establishing an analyzable evaluation system with constraint timing; and using a constraint evaluation model to trace sequential change of physiological parameters, combing a preset rule base and sequential change information, rating the signal quality of the quasi-periodic physiological signal, evaluating the validity of signal data of the signal sections of the quasi-periodic physiological signal, updating a time sequence evaluation system, and rating according to iteration of the periodic signal sections until the signal quality rating of all the signal sections of the quasi-periodic physiological signal is finished.