Objective To study the influence of middle ear malformation on the performance of round window stimulation, and provide reference for the optimization of round window stimulation middle ear implant. Methods A human ear finite element model including an asymmetrical two-cavity non-helical cochlea was constructed and compared with experimental data to verify the reliability of the model. Based on the model, the effects of three kinds of middle ear malformations,i.e., ossicular chain fixation, ossicular chain fusion and ossicular defect on the round window stimulation were simulated by changing the material properties of the corresponding tissues. Results The middle ear malformation mainly affects the low-frequency performance of the round window stimulation. The ossicular chain fixation and the ossicular chain fusion have a deteriorating effect on the round window stimulation. Among them, the stapes fixation has the greatest deterioration of the round window stimulation’s performance. Ossicles defects can boost the performance of round window stimulation. Conclusions The middle ear malformation has an effect on the low frequency performance of the round window stimulation. When designing the round window stimulation type middle ear implant, it is necessary to increase the output of its actuator accordingly.