Implantable deep brain probes (DBPs) constitute a vital component of brain-machine interfaces, facilitating direct interaction between neural tissues and the external environment. Most multifunctional DBPs used for neural system sensing and modulation are currently fabricated through thermal tapering of polymeric materials. However, this approach faces a fundamental challenge in selecting materials that simultaneously accommodate the thermal stretching process and yet match the modulus of brain tissues. Here, we introduce a kind of multifunctional hydrogel-based fiber (HybF) designed for neural sensing, on-demand deep brain manipulation, and photodynamic therapy, and was achieved by integrating ion chelation/dechelation effects with templating methods throughout the entire wet-spinning process. With a low bending stiffness of approximately 0.3 N/m and a high conductivity of about 97 S/m at 1 kHz, HybF facilitates a high-quality signal recording (SNR ∼10) while minimizing immune rejection. It also effectively mediates deep brain optogenetic stimulation, successfully manipulating the behavior of hippocampal neurons in hSyn-ChrimsonR-tdTomato SD rats. Importantly, by leveraging HybF, this study explores the use of a spatiotemporally controllable photodynamic strategy in antiepilepsy, in which the high-amplitude abnormal electrical discharges were instantaneously eliminated without affecting normal cognitive/memory abilities. The above innovative approach established a distinct paradigm for deep brain manipulation and degenerative disease treatment, providing interesting insights into brain circuits and bioelectronic devices.