Objective To explore the differences between the results of the two commonly-used algorithms for estimating muscle forces, i.e., static optimization (SO) and computational muscle control (CMC), so as to provide basis for researchers to choose the appropriate one in movement analysis and compare the results from different studies. Methods Two algorithms were used to calculate the forces and activations of the major muscles in lower limbs in a single running gait cycle at four different speeds and the results were compared. Results Among the 10 major muscles participating in running, except for anterior tibial and rectus femoris, the muscle forces and muscle activations solved by the two algorithms had similar curves with correlation coefficients more than 0.91, and the peak value of muscle forces solved by SO was higher and the positions of peak muscle activation had a certain delay (~0.01 seconds). Conclusion In movement analysis, if the research focuses on the timing of muscle forces and the contribution ratios among different muscles, there is not too much difference and SO is recommended for its simplicity and efficiency. When comparing the muscle forces and muscle activations estimated by the two algorithms in different studies, the differences between them should be considered.