3D NAND is one of the most promising storage devices due to its high storage density and low energy consumption. Selective wet etching of Si3N4 by hot-concentrated phosphoric acid (PA) solution is a key process for 3D NAND fabrication. However, the channel material, polycrystalline silicon (poly-Si), is unexpectedly dissolved due to its inevitable exposure to the PA etching solution, which causes device failure and thus limits the stacking density of 3D NAND. Herein, to avoid the detrimental dissolution of poly-Si, we unveil the mechanism of poly-Si dissolution in PA solution from kinetic and thermodynamic perspectives. We find that the etch process shows a two-stage reaction, in which H2O plays a key role in lowering the activation barrier for poly-Si etching. Further thermodynamic analysis demonstrates that poly-Si prefers to be oxidized by H2O to suboxide rather than to SiO2. Combined with surface chemistry characterization, we propose the dissolution mechanism as a two-stage process involving the dissolution of suboxide interface and bulk poly-Si, where the nucleophilic substitution of Si–H with Si–OH on bulk poly-Si surface determines the overall etch rate. This study advances the 3D NAND development by establishing a theoretical foundation for identifying and implementing efficacious strategies to impede detrimental dissolution.