Simultaneous monitoring of electrophysiology and magnetic resonance imaging (MRI) could guide the innovative diagnosis and treatment of various neurodegenerative diseases that were previously impossible. However, this technique is difficult because the existing metal‐based implantable neural interface for electrophysiology is not free from signal distortions due to its intrinsic magnetic susceptibility while performing an MRI of the implanted area of the neural interface. Moreover, brain tissue heating from neural implants generated by the radiofrequency field from MRI poses potential hazards for patients. Previous studies with soft polymer‐based electrode arrays that overcome this issue provided relatively suitable MRI compatibility but did not guarantee high‐resolution electrophysiological signal acquisition and stimulation performance. Here, we introduce MRI compatible, optically transparent flexible implantable device capable of electrophysiological multichannel mapping and electrical stimulation. Using the device, we confirmed neuropathic pain (NP) relief with a 30‐channel electrophysiological mapping of the somatosensory area before and after motor cortex stimulation (MCS) in allodynia rats after noxious stimulation. Additionally, we demonstrated artifact‐free manganese‐enhanced MRI of dramatic relief of pain‐related region activity by MCS. Furthermore, artifact‐free optogenetics with transgenic mice was also investigated by recording light‐evoked potentials. These results suggested a promising neuro‐prosthetic for analyzing and modulating spatiotemporal neurodynamic without MRI or optical modality resolution constraints.This article is protected by copyright. All rights reserved.