Electric stimulation of auditory nerve by cochlear implants has been a successful clinical intervention to treat the sensorineural deafness. However, various micro-anatomical factors have not been considered in the state of the art models while studying the interaction between the applied electric field and the auditory nerve. The present finite element modeling study suggests that the modiolus porosity and tissue heterogeneity significantly alter the electric field distribution in the Rosenthal’s canal and thereby affect the cochlear implant functionality.