Objective To explore the differences between the result of static optimization (SO) and computational muscle control (CMC) algorithms for estimating muscle forces, so as to provide references for researchers to choose the appropriate algorithm and make horizontal comparison of the results from different studies. Methods Targeting at a single gait cycle running at four different speeds, SO and CMC algorithms were used to calculate forces and activations of the major muscles in lower limbs, and the results were compared and analyzed. Results Among the 10 major muscles participating in running, except for anterior tibial and rectus femoris, 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 10 ms delay. Conclusions In movement analysis, if the research focuses on the timing of muscle forces and the contribution ratios among different muscles, there is not too big difference and SO algorithm is recommended for its simplicity and efficiency. For horizontal comparison of muscle forces and muscle activations estimated by SO and CMC algorithms in different studies, the differences between the two algorithms should be considered.