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The boundary element method (BEM) and sequential function specification method (SFSM) are used to research the inverse problem of boundary heat flux identification in the two-dimensional heat conduction system. The future time step in the SFSM is optimized by introducing the residual error principles to get the more accurate inversion results. For the forward problems, the BEM is used to calculate the required temperature value of discrete point; for the inverse problems, the impacts of different future time steps, measuring point position, and measuring error on the inversion results are discussed. Furthermore, the comparison is made for the optimal future time step obtained by introducing the residual error principle and the inherent future time step. The example analysis shows that the method proposed still has higher accuracy when the measuring error exists or the measuring point position is far away from the boundary heat flux.