The invention provides a heat compensation method for wafer annealing. A spacer is formed on each gate of each wafer. For each wafer, the thickness of the spacer is measured, and temperature compensation is made for the wafer during spike annealing of the wafer according to the change Delta(D) of spacer thickness. The compensated temperature Delta(T) equals to a*Delta(D)+b, wherein a and b are the influence coefficients of the spacer thickness change Delta(D) and the spike annealing temperature change Delta t on electrical parameters. As wafers are inconsistent in spacer thickness in production, the invention designs a temperature compensation formula Delta(T)=a*Delta(D)+b based on the spacer thickness change of each wafer. The temperature is compensated differently for different wafers and different spacer thicknesses. Thus, different wafers are heated consistently. The electrical parameters of semiconductor devices manufactured through the process are stabilized within a certain range, which brings convenience to subsequent test and application.