Bilayer structure with functional overlayer has been commonly adopted to resolve the issue of moisture poisoning in chemiresistors. However, the conventional overlayers always suffer from blocking access of gas molecules to sensing layer due to lacking porosity and deteriorated adsorption capability. Herein, taking advantages of the well-defined porous structure and hydrophobic nature of pure silica zeolite, we assembled an overlayer of Pd-PdO clusters-encapsulated mesoporous silicalite-1 (MFI) zeolite (named M-S-1) on ZnO sensing layer, to prevent moisture poisoning, and enhance gas diffusion and adsorption capabilities. The inherent capability of MFI zeolite to incorporate monodispersed nanometric (ca. 3 nm) Pd-PdO cluster in its void space is of great importance for the NO₂ adsorption. The Pd-PdO@M-S-1 overlayer can attain negligible moisture interference to the ZnO layer without significantly altering the gas selectivity and baseline resistance, and enhance gas response. Consequently, the Pd-PdO@M-S-1/ZnO bilayer sensor can ultra-selectively (S_{nitrogen dioxide}/S_{interference gas} > 4), and ultra-stably detect trace level of NO₂ (9.5 ppb) at low temperature (370 K) under high levels of humidity (90% RH). This work exemplifies a next-generation solution to design bilayer sensors using zeolite overlayer for eliminating the humidity dependence of the gas-sensing properties.