Driving the electrochemical carbon dioxide reduction reaction (CO2RR) to generate high-value chemicals is one of the effective solutions to promote carbon–neutral cycles. Herein, we use a heterostructure strategy to enhance the catalytic performance of single-atom catalysts (SACs) for CO2RR. A series of catalysts formed by doping some transition metal atoms (TM = Cr, Mn, Fe, Co, Ni, Cu) into heterostructures which include the single-wall carbon nanotube in boron nitride nanotube (CNT@BNNT) and the hybridization of carbon nanotube and boron nitride nanotube (CNT/BNNT) are respectively named as TM-CNT@BNNT and TM-CNT/BNNT, and their catalytic activity of CO2RR is systematically studied using density functional theory methods. After forming a heterostructure, the number of charges transferred from the metal center to the substrate and the d-band center will change, which will, to some extent, regulate the catalytic activity of the catalyst. Due to the effective activation of CO2 and significant inhibition ability of competitive hydrogen evolution reaction, nine catalysts are considered effective candidates for CO2RR. Finally, seven catalysts with high CO2RR activity are selected by calculating the Gibbs free energy. The moderate linear relations between charge transfer and adsorption energy of CO2/free energy change of reaction intermediates/limiting potential indicate that charge transfer can regulate activity to a certain extent. The improvement of CO2RR activity comes from the smaller charge transfer in the metal center, which is more likely to result in moderate binding strength between the catalyst and the key intermediate (*OH) to generate high catalytic performance.