For high-performance mixed-matrix membranes (MMMs), it is crucial to design gas transport channels in fillers to rationally manipulate the structure-property relationship. In this study, the novel porous organosilicon nanotubes (PSiNTs) were incorporated into Pebax to prepare MMMs for biogas purification (CO/CH separation). After comparing the separation performance of MMMs containing PSiNTs and MMMs containing non-porous organosilicon nanotubes (SiNTs)，it can be found that the porous structure on wall of organosilicon nanotubes had a significant effect on the improvement of the gas permeability. In addition, the amino-modified PSiNTs (N-PSiNTs) were prepared and introduced into membranes to significantly enhance the CO permeability and CO/CH selectivity. Firstly, the porosity of N-PSiNTs afforded rapid gas transport channels in MMMs and intensified the diffusion mechanism, increasing the CO permeability. Secondly, the reversible reaction between amino groups and CO in MMMs intensified the facilitated transport mechanism, increasing the CO/CH selectivity. In particular, the Pebax-N-PSiNTs with 0.5 wt% and 1 wt% N-PSiNTs exhibited the optimal separation performance, which surpassed 2008 upper bound and were superior to the MMMs incorporated with other kinds of nanotubes.