The invention discloses a temperature compensation method of a system for detecting heavy metals in a water environment. After acquired polarization current and polarization potential are subjected to smoothing processing through differential filtering, a fitted regression equation inverse model is established, a temperature compensation model is obtained through solution of the deviation, the square deviation and the partial derivative, judgment is performed in combination with the REF (relative error factor), the number of fitting times is increased automatically for fitting again when the standard is not met, a high-order multivariate regression inverse model with the higher precision is constructed, the temperature compensation model is applied to detection of the heavy metals in the water environment, and the detection precision can be improved.