Bioelectronic devices made of soft elastic materials exhibit motion-adaptive properties suitable for brain-machine interfaces and for investigating complex neural circuits. While two-dimensional microfabrication strategies enable miniaturizing devices to access delicate nerve structures, creating 3D architecture for expansive implementation requires more accessible and scalable manufacturing approaches. Here we present a fabrication strategy through the control of metamorphic polymers’ amorphous-crystalline transition (COMPACT), for hydrogel bioelectronics with miniaturized fiber shape and multifunctional interrogation of neural circuits. By introducing multiple cross-linkers, acidification treatment, and oriented polymeric crystalline growth under deformation, we observed about an 80% diameter decrease in chemically cross-linked polyvinyl alcohol (PVA) hydrogel fibers, stably maintained in a fully hydrated state. We revealed that the addition of cross-linkers and acidification facilitated the oriented polymetric crystalline growth under mechanical stretching, which contributed to the desired hydrogel fiber diameter decrease. Our approach enabled the control of hydrogels’ properties, including refractive index (RI 1.37-1.40 at 480 nm), light transmission (> 96%), stretchability (95% - 111%), and elastic modulus (10-63 MPa). To exploit these properties, we fabricated step-index hydrogel optical probes with contrasting RIs and applied them in optogenetics and photometric recordings in the mouse brain region of the ventral tegmental area (VTA) with concurrent social behavioral assessment. To extend COMPACT hydrogel multifunctional scaffolds to assimilate conductive nanomaterials and integrate multiple components of optical waveguide and electrodes, we developed carbon nanotubes (CNTs)-PVA hydrogel microelectrodes for hindlimb muscle electromyographic and brain electrophysiological recordings of light-triggered neural activities in transgenic mice expressing Channelrhodopsin-2 (ChR2).