An effective surface cleaning technique is demonstrated for the GaN metal-insulator-semiconductor high-electron-mobility transistor (MIS-HEMT) passivation process. In this study, dilute HF solution and in situ N2 plasma treatments were adopted to remove the native oxide and recover the nitrogen-vacancy defects at the GaN surface before device passivation. To investigate the correlation between the properties of the SiN/GaN interface and the device performance, the GaN MIS-HEMTs were characterized using current-voltage (I-V) measurement, capacitance-voltage (C-V) measurement, and X-ray photoelectron spectroscopy (XPS) analysis. With the application of this surface treatment technique, the device exhibits improved I-V characteristics with low leakage current, low dynamic ON-resistance, and good C-V response with a steep slope. Overall, the results reveal that the oxide-related bonds and nitrogen-vacancy defects at the SiN/GaN interface are the root cause of the GaN MIS-HEMTs performance degradation.