The efficient conversion of CO2 into hydrocarbon fuels (CH4) with high selectivity is considered as a great challenge in photocatalysis owing to the multiple-electron transfer pathway and competitive H2 generation. Herein, we developed carbon dots (CDs)-modulated S-scheme heterojunction of CDs/NiAl-LDH@In2O3 (C-DH@IN) through a facile in-situ hydrothermal method. Thanks to the multi-shell nanotube structure, the C-DH@IN shows an enhanced CH4 evolution rate of 10.67 µmol h−1 g−1 and higher selectivity of CH4 (85.70%) compared with In2O3 and NiAl-LDH@In2O3 binary catalyst in the pure water without sacrificial agent. Electron spin resonance (ESR) and in situ Fourier transform infrared spectra verify that the constructed S-scheme heterojunction can possess the strong redox capability and the HCOO− and CH3O− as critical intermediates play an important role in selective CO2 reduction to generate CH4. Furthermore, CDs with superior photoabsorption can boost the electron transfer and absorb H+, thus improving the integration of H+ and CO2 molecule. Therefore, this work emphasizes a facile strategy to achieve efficient CO2-to-CH4 conversion based on construction of CDs-based heterojunction catalysts.