In a high vacuum environment, some organic molecular pollutants such as hydrocarbon and siloxane are released by spacecraft materials and deposited on the surface of the sensitive parts of spacecraft devices, which has become an important adverse factor restricting the development of long-life and high-performance spacecraft. Zeolite molecular adsorber coating can effectively collect spatial contaminations in real time, but the adsorption mechanism is not clear. To deeply analyze the adsorption mechanism of zeolite on the spatial contaminations, the adsorption behaviors of NaY zeolite including adsorption isotherms, adsorption heat curves and density distributions on three typical contaminations, toluene(C₇H₈), dimethyl phthalate (C₁₀H₁₀O₄), octamethyl cyclotetrasiloxane (C₈H₂₄O₄Si₄), were calculated by the Grand Canonical Monte Carlo method in this work. The NaY zeolites and pollutant models were successfully constructed, and the rationality of the models was verified by comparing simulated data with experimental ones. These results indicated that all three classic molecules can be adsorbed by NaY zeolite in the ultra-high vacuum condition. The saturated adsorption capacity decreases in the order of C₇H₈>C₁₀H₁₀O₄>C₈H₂₄O₄Si₄, which is significantly related to the molecule sizes and structures of contaminations. The saturated adsorption amount of C₈H₂₄O₄Si₄ is relatively low (8 per cell) when that of C₇H₈ is 36 per cell. In addition, the density distributions indicates that different contaminations are preferentially adsorbed inside the super-cage of NaY zeolite. Overall, this work analyzes the adsorption mechanism of NaY zeolite on typical contaminations, and can provide basic insights for the development of zeolite molecular adsorber coating with high adsorption capacity.