Background: Although numerous studies have been conducted to investigate the acute effects of shoe drops on running kinematics and kinetic variables, their effects on muscle forces remain unknown. Thus, the primary aim of this study was to compare the muscle force, kinematics, and kinetic variables of habitually rearfoot runners with heel-to-toe drops of negative 8 mm shoes (minimalist shoes) and positive 9 mm shoes (normal shoes) during the running stance phase by using musculoskeletal modeling and simulation techniques. Methods: Experimental data of lower limb kinematics, ground reaction force, and muscle activation from 16 healthy runners with rearfoot strike patterns were collected and analyzed in OpenSim. Using Matlab, the statistical parameter mapping paired t-test was used to compare the joint angle, moment, and muscle force waveform. Results: The results revealed differences in the sagittal ankle and hip angles and sagittal knee moments between the different heel-to-toe drops of running shoes. Specifically, it showed that the negative 8 mm running shoes led to significantly smaller values than the positive 9 mm running shoes in terms of the angle of ankle dorsiflexion, ankle eversion, knee flexion, hip flexion, and hip internal and hip external rotation. The peak ankle dorsiflexion moment, ankle plantarflexion moment, ankle eversion moment, knee flexion moment, knee abduction moment, and knee internal rotation also decreased obviously with the minimalist running shoes, while the lateral gastrocnemius, Achilleas tendon, and extensor hallucis longus muscles were obviously greater in the minimalist shoes compared to normal shoes. The vastus medialis, vastus lateralis and extensor digitorum longus muscles force were smaller in the minimalist shoes. Conclusions: Runners may shift to a midfoot strike pattern when wearing negative running shoes. High muscle forces in the gastrocnemius lateral, Achilleas tendon, and flexor hallucis longus muscles may also indicate an increased risk of Achilleas tendonitis and ankle flexor injuries.