Retinal implants have been developed and implanted to restore vision from outer retinal degeneration, but their performance is still limited due to the poor spatial resolution. To improve the localization of stimulation, microelectrodes in various three-dimensional (3D) shapes have been investigated. In particular, computational simulation is crucial for optimizing the performance of a novel microelectrode design before actual fabrication. However, most previous studies have assumed a uniform conductivity for the entire retina without testing the effect of electrodes placement in different layers. In this study, we used the finite element method to simulate electric fields created by 3D microelectrodes of three different designs in a retina model with a stratified conductivity profile. The three electrode designs included two conventional shapes - a conical electrode (CE) and a pillar electrode (PE); we also proposed a novel structure of pillar electrode with an insulating wall (PEIW). A quantitative comparison of these designs shows the PEIW generates a stronger and more confined electric field with the same current injection, which is preferred for high-resolution retinal prostheses. Moreover, our results demonstrate both the magnitude and the shape of potential distribution generated by a penetrating electrode depend not only on the geometry, but also substantially on the insertion depth of the electrode. Although epiretinal insertions are mainly discussed, we also compared results for subretinal insertions. The results provide valuable insights for improving the spatial resolution of retinal implants using 3D penetrating microelectrodes and highlight the importance of considering the heterogeneity of conductivities in the retina.