Objective To study the influence of middle ear malformation on the performance of round window stimulation, so as to provide references for optimization of the round window stimulation middle ear implant. Methods The finite element model of human ear including an asymmetrical two-cavity non-helical cochlea was constructed and compared with experimental data to verify reliability of the model. Based on this model, the effects of three kinds of middle ear malformation, i.e., ossicular chain fixation, ossicular chain fusion and ossicular defect on round window stimulation were simulated by changing material properties of the corresponding tissues. Results The middle ear malformation mainly affected the low-frequency performance of round window stimulation. The ossicular chain fixation and the ossicular chain fusion had a deteriorating effect on round window stimulation. The stapes fixation had the greatest effect on the performance of round window stimulation, with the reduction as high as 47.93 dB. Ossicles defects could improve the performance of round window stimulation, with the maximum increment of 6.24 dB. Conclusions The middle ear malformation had an effect on the low frequency performance of round window stimulation. It is necessary to specifically increase output of the actuator when implanting the round window stimulation middle ear implant.