An integration strategy is devised for a reliable, scalable, and catalyst-free assembly of SiOxNy nanowires in photoresist-derived carbon microelectrodes. The approach involved UV photolithography process of SU8 photoresist, followed by high-temperature carbonization, and was versatile in yielding various 3-D micro-nano integrated carbon microelectrode arrays (CMEAs). The morphology of the SiOxNy nanowires and the nanowire-integrated CMEA was characterized by scanning electron microscopy and high-resolution transmission electron microscopy. The chemical composition of the SiOxNy nanowires was confirmed by energy-dispersive X-ray and X-ray photoelectron spectroscopy. A synergetic growth mechanism is proposed based on our experimental observations, in which both carbon-assisted and stress-driven mechanisms were identified to interpret the formation of SiOxNy nanowires. Further study revealed that the nanowire-integrated 3-D CMEA showed improved electrical and electrochemical performances than the blank ones, demonstrating potential applications in electrochemical, biological, and energy-related fields. Meanwhile, the developed method represents a low-cost and easy way to mass production of SiOxNy nanowire-integrated CMEA.