The miniaturization and integration of electronic devices have led to the increase of chips heat flux, making heat dissipation in confined spaces increasingly challenging. Silicon-based vapor chambers (VC) provide a simple, reliable, and easily integrable solution. An ultra-thin silicon-based VC with dimensions of 7 mm × 7 mm × 0.6 mm was designed and fabricated in this study. An experimental system was set up to investigate the impact of three working fluids (2100A, anhydrous ethanol, and deionized water) on the heat transfer performance of the silicon-based VC. Experimental results show that the silicon-based VC using anhydrous ethanol has the lowest thermal resistance, reducing thermal resistance by 61.4% compared to the unfilled VC. Additionally, the silicon-based VC using deionized water demonstrates the best temperature uniformity performance under high heat loads.