In this paper, the effects of a thin in-situ SiNx layer, grown by metal–organic chemical vapor deposition (MOCVD), on the performances of GaN-based metal-insulator-semiconductor high electron mobility transistors (MIS-HEMTs) with low-pressure chemical vapor deposition (LPCVD) SiNx gate dielectric were systematically investigated. We found that the MIS-HEMT with the in-situ SiNx as an interface sacrificial layer exhibits better DC electrical properties than that with the in-situ SiNx reserved as part of the gate dielectric. The results of second ion mass spectroscopy and electron spin resonance spectrum show that this in-situ SiNx is a Si-rich SiNx dielectric which can induce additional ≡Si0 and ≡Si- trap states by Si dangling bonds and affects significantly electron trapping and detrapping processes. Based on temperature-dependent gate current and frequency-dependent capacitance-voltage analyses, a trap model at the SiNx/AlGaN interface and in the in-situ SiNx bulk was proposed and well explains the performance discrepancies between the above mentioned two MIS-HMETs. In addition, positive bias temperature instability was carried out to further confirm the rationality of the proposed trap model. This work verifies that in-situ SiNx can be employed as a sacrificial layer for the fabrication of high performance LPCVD-SiNx/AlGaN/GaN MIS-HEMTs.