Including servo valve, hydraulic cylinder, mill and sensor and ignoring nonlinear factors, the linear dynamic model of hydraulic automatic gage control(HAGC) system of a temper rolling mill was theoretically derived. The order of the model is 4/4, and can be reduced to 2/2. Based on modulating functions method, utilizing numerical integration, we constructed the equivalent identification model of HAGC, and the least square estimation algorithm was established. The input and output data were acquired on line at temper rolling mill in Shangshai Baosteel Group Corporation, and the continuous time model of HAGC system was estimated with the proposed method. At different modulating window intervals, the estimated parameters changed remarkably. When the frequency bandwidth of modulating filter matches that of estimated system, the parameters can be estimated accurately. Finally, the dynamic model of the HAGC was obtained and validated based on the spectral analysis result.