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Implantable brain electrophysiology electrodes are valuable tools in both fundamental and applied neuroscience due to their ability to record neural activity with high spatiotemporal resolution from shallow and deep brain regions. Their use has been hindered, however, by the challenges in achieving chronically stable operations. Furthermore, implantable depth neural electrodes can only carry out limited data sampling within predefined anatomical regions, making it challenging to perform large-area brain mapping. Minimizing inflammatory responses and associated gliosis formation, and improving the durability and stability of the electrode insulation layers are critical to achieve long-term stable neural recording and stimulation. Combining electrophysiological measurements with simultaneous whole-brain imaging techniques, such as magnetic resonance imaging (MRI), provides a useful solution to alleviate the challenge in scalability of implantable depth electrodes. In recent years, various carbon-based materials have been used to fabricate flexible neural depth electrodes with reduced inflammatory responses and MRI-compatible electrodes, which allows structural and functional MRI mapping of the whole brain without obstructing any brain regions around the electrodes. Here, we conducted a systematic comparative evaluation on the electrochemical properties, mechanical properties, and MRI compatibility of different kinds of carbon-based fiber materials, including carbon nanotube fibers, graphene fibers, and carbon fibers. We also developed a strategy to improve the stability of the electrode insulation without sacrificing the flexibility of the implantable depth electrodes by sandwiching an inorganic barrier layer inside the polymer insulation film. These studies provide us with important insights into choosing the most suitable materials for next-generation implantable depth electrodes with unique capabilities for applications in both fundamental and translational neuroscience research.