Two-dimensional materials as emerging nano-building blocks for constructing channels with high gas permselectivity in membranes have drawn increasing attention, which is ascribed to their atomic thickness and extraordinary physicochemical properties. Nevertheless, manufacturing lamellar membranes with precise sub-nano channels and abundant facilitate groups for fast CO2 transport remains a challenge. Herein, we develop an ultrathin lamellar stacked vermiculite (VMT) membrane with amino acid intercalation via vacuum-assisted self-assembly approach for biogas upgrading. The vermiculite possesses exchangeable cations between its adjacent layers, which provides the possibility that makes the amino acid with positive charge intercalate into the interlayers, thus constructing regular and tunable nanochannels with abundant facilitated transport carriers. Moreover, amino acid has excellent water retention capacity, effectively adjusting the chemical microenvironment of nanochannels. Elevating the selective diffusion of CO2 and CH4 can be realized through regulating the interlayer channel size in VMT membranes. Facilitated transport mechanism is incorporated as a result of the reversible reaction between carboxylate and amino groups on amino acids and CO2. By means of synergistically enhancing selective diffusion and facilitated transport mechanisms, the resultant membrane possesses a high CO2 permeance about 330 GPU with the CO2/CH4 selectivity of 32.1, and good long-term operation stability over 200 h.