The invention provides a parameter-estimation-based harmonic wave analyzing system which belongs to the harmonic wave analyzing technology field and comprises branch channels, a multi-channel comprehensive determining module, a saving module and a displaying module. Each group of the branch channels is provided with a data source module, a sequence generator and a parameter estimation module. The signal output ends of the parameter estimation modules of each group of branch channels are connected with the signal input end of the multi-channel comprehensive determining module respectively. According to the invention, a parameter estimation theory is introduced so as to obtain the equivalent impedance and equivalent harmonic electromotive force key information of a power grid harmonic wave. As the traditional manual intervention analysis becomes intelligent assistance, the analyzing efficiency is increased; and the harmonic wave analysis becomes more discrete. The system of the invention also provides diversified input and output formats; the input in the offline analyzing work mode can be historical data; and the input in the online analyzing work mode can be real time measured data. The system can be applied to various occasions flexibly.