Reliable insulation of microscale conductive features is required to fabricate functional multilayer circuits or flexible electronics for providing specific physical/chemical/electrical protection. However, the existing strategies commonly rely on manual assembling processes or multiple microfabrication processes, which is time-consuming and a great challenge for the fabrication of flexible transparent electronics with microscale features and ultrathin thickness. Here, we present a novel coaxial electrohydrodynamic (CEHD) printing strategy for the one-step fabrication of microscale flexible electronics with conductive materials at the core and insulating material at the outer layer. A finite element analysis (FEA) method is established to simulate the CEHD printing process. The extrusion sequence of the conductive and insulating materials during the CEHD printing process shows little effect on the morphology of the core-shell filaments, which can be achieved on different flexible substrates with a minimum conductive line width of 32 ± 3.2 μm, a total thickness of 53.6 ± 4.8 μm, and a conductivity of 0.23 × 107 S/m. The thin insulating layer can provide the inner conductive filament enough protection in 3D, which endows the resultant microscale core-shell electronics with good electrical stability when working in different chemical solvent solutions or under large deformation conditions. Moreover, the presented CEHD printing strategy offers a unique capability to sequentially fabricate an insulating layer, core-shell conductive pattern, and exposed electrodes by simply controlling the material extrusion sequence. The resultant large-area transparent electronics with two-layer core-shell patterns exhibit a high transmittance of 98% and excellent electrothermal performance. The CEHD-printed flexible microelectrode array is successfully used to record the electrical signals of beating mouse hearts. It can also be used to fabricate large-area flexible capacitive sensors to accurately measure the periodical pressure force. We envision that the present CEHD printing strategy can provide a promising tool to fabricate complex three-dimensional electronics with microscale resolution, high flexibility, and multiple functionalities.