There are some restrictions in the two sources estimation problem in recent studies. One of the restrictions is that the estimated results are inaccurate when two sources have different shapes and close distance. Another is that the accuracy of the estimation is questioned when the duration of two heat sources has a significant difference. The third restriction is that the estimation becomes inaccurate when the ratio of the peak values of the two heat sources is too large. Therefore, it is necessary to develop a robust method to estimate the strengths of two heat sources in order to alleviate the problems in past research. In this paper, a numerical algorithm coupled with the concept of future time is proposed to determine the problem sequentially. A special feature about this method is that no preselect functional form for the unknown sources is necessary and no sensitivity analysis is needed in the algorithm. Three examples are used to demonstrate the characteristics of the proposed method. From the results, they show that the proposed method is an accurate and efficient method to determine the strength of the two sources in the inverse heat conduction problems.