Synaptic exocytosis requires efficient SNARE complex assembly that is precisely regulated by multiple regulatory proteins. Increasing evidence suggests that Munc18-1 and Munc13-1 protect SNARE complex assembly in a manner resistant to NSF and α-SNAP. However, the protective mechanisms of Munc18-1 and Munc13-1 are not fully understood. Here, by analyzing two pathways of SNARE complex assembly (i.e., the Munc18 - Munc13-dependent pathway and the Munc18 - Munc13-independent pathway), we found that the Munc18 - Munc13-dependent pathway of SNARE complex assembly is resistant to NSF - α-SNAP. In this pathway, Munc18-1 and Munc13-1 each, independently, have protective effects. The protective effect of Munc18-1 relies on the interaction with the C-terminal part of Syb2 during the transition from the Munc18-1/Syx1 complex to the SNARE complex. Moreover, the protective effect of Munc13-1 is most likely attributed to its ability in templating the assembling SNAREs. In addition, we found that the Munc18 - Munc13-dependent pathway opposes the association of α-SNAP with the SNARE bundle, thus explaining how this pathway is resistant to NSF - α-SNAP disassembly. Although the above results were derived from the studies on SNARE complex in solution or in cis-configurations, instead of trans-configurations residing on the opposite membrane, our data could still help to understand the protective mechanism of Munc18-1 and Munc13-1 in SNARE-mediated synaptic exocytosis.