The performance of boron nitride nanotubes (BNNTs) and carbon nanotubes (CNTs) in multiple gas separation systems was systematically compared using molecular simulation methods. Findings reveal that under conditions of 298 K and 2 MPa, BNNTs generally show higher adsorption selectivities than CNTs for CH4/N2, CO2/CH4, and CO2/N2 mixtures. Notably, in the CO2/CH4 system, BNNTs exhibit a selectivity of up to 350 at a radius of 0.48 nm, significantly surpassing the 14 observed for CNTs; in the CO2/N2 system, selectivity can reach as high as 969 for BNNTs, contrasting with the 69 for CNTs. Furthermore, BNNTs achieve saturation adsorption for CF4 at 0.04 MPa with a capacity of 2.7 mmol/g, while CNTs show a higher adsorption capacity for N2, reflecting the superior selective adsorption capability of BNNTs for specific gases. Analysis of nanotubes with different chiral configurations led to the recommendation of (11,11) and (7,7) chiralities as optimal structures for efficient gas separation. Fluctuations in energy contributions from fluid-wall interactions in BNNTs, are closely related to their selectivity fluctuations. The results demonstrate that BNNTs, due to their unique structural characteristics, possess significant potential in the field of gas adsorption and separation, particularly in enhancing the selective adsorption of CO2 and CF4.