Both CH4 hydrate accumulation and hydrate-based CO2 sequestration involve hydrate formation in mixed clay sediments. The development of realistic clay models and a nanoscale understanding of hydrate formation in mixed clay sediments are crucial for energy recovery and carbon sequestration. Here, we propose a novel molecular model of pseudo-hexagonal montmorillonite nanoparticles. The stress–strain curves of tension, compression, and shear of pseudo-hexagonal montmorillonite nanoparticles exhibit linear characteristics, with tension, compression, and shear moduli of ∼435, 410, and 137 GPa, respectively. We perform microsecond molecular dynamics simulations to study CH4 and CH4/CO2 hydrate formation in montmorillonite–illite mixed clay sediments with surface defects. The results indicate that hydrate formation in mixed clay sediments is significantly influenced by the presence of clay defects. CH4 and CH4/CO2 mixed hydrates are challenging to form at the junction between the inside and outside clay defects. CH4 and CH4/CO2 mixed hydrates exhibit a preference for forming outside the clay defects rather than inside the clay defects. Some CH4 and CO2 molecules from the inside clay defect migrate to the outside clay defect, thereby promoting CH4 and CH4/CO2 mixed hydrate formation outside the clay defects. This molecular insight advances the development of clay particle models and expands an understanding of natural gas hydrate accumulation and hydrate-based CO2 sequestration.