How the state of living muscles modulates the features of nonlinear elastic waves generated by external dynamic loads remains unclear because of the challenge of directly observing and modeling nonlinear elastic waves in skeletal muscles in vivo, considering their active deformation behavior. Here, this important issue is addressed by combining experiments performed with an ultrafast ultrasound imaging system to track nonlinear shear waves (shear shock waves) in muscles in vivo and finite element analysis relying on a physically motivated constitutive model to study the effect of muscle activation level. Skeletal muscle was loaded with a deep muscle stimulator to generate shear shock waves (SSWs). The particle velocities, second and third harmonics, and group velocities of the SSWs in living muscles under both passive and active states were measured in vivo. Our experimental results reveal, for the first time, that muscle states have a pronounced effect on wave features; a low level of activation may facilitate the occurrence of both the second and third harmonics, whereas a high level of activation may inhibit the third harmonic. Finite element analysis was further carried out to quantitatively explore the effect of active muscle deformation behavior on the generation and propagation of SSWs. The simulation results at different muscle activation levels confirmed the experimental findings. The ability to reveal the effects of muscle state on the features of SSWs may be helpful in elucidating the unique dynamic deformation mechanism of living skeletal muscles, quantitatively characterizing diverse shock wave-based therapy instruments, and guiding the design of muscle-mimicking soft materials.