Silicon nitride (Si3N4) ceramic has excellent durability and superior outstanding mechanical properties, which makes it extensively applied in aerospace, biopharmaceuticals, semiconductors and optoelectronics. Nevertheless, the precise microfabrication of complex-shaped Si3N4 microgrooves, particularly those with large aspect-ratio (LAR) presents significant challenges, and traditional machining methods fall short in meeting the demanding criteria for high-precision applications due to the difficult-to-machine characteristics (e.g. high hardness, high strength and brittleness, etc.). In this research, waterjet-assisted laser machining (WJALM) is preferably adopted for LAR Si3N4 microstructures, which has demonstrated superiority in reducing thermal-induced defects of laser-only machining (LOM) with the water's impact and cooling effects. A comparative investigation of LOM and WJALM is initially conducted to evaluate the heat-affected zone (HAZ), geometric characteristics and sidewall surface quality of LAR Si3N4 microgrooves. Following that, the influence of waterjet and laser parameters on morphological characteristics for WJALM is studied through the control variable method. Results indicated that compared to LOM, the HAZ, material removal rate and sidewall surface quality of LAR microgrooves fabricated by WJALM were much superior. This research not only provides new strategies for Si3N4 microgrooves but also lays the foundation for the further development and industrial application of water-assisted laser technology.