Associating molecular structure and mechanical properties is important for silicone rubber design. Although silicone rubbers are widely used due to their odourless, non-toxic, and high- and low-temperature resistance advantages, their application and development are still limited by their poor mechanical properties. The mechanical properties of silicone rubbers can be regulated by designing the cross-link density and cross-linking structure, and altering the molar contents of vinyl in the side groups of methyl vinyl silicone rubber (MVQ) leads to different cross-linking structures and cross-linking densities in the vulcanized rubber. Therefore, this study investigated the differences in molecular parameters and molecular chain structures of unprocessed MVQ rubbers with different vinyl contents. The results showed that MVQ rubbers with high vinyl contents were branched polymers, better facilitating the cross-linking reaction than MVQ rubbers with low vinyl contents. In addition, silicone rubbers with different vinyl contents were co-cross-linked to introduce an inhomogeneous cross-linked network in the silicone rubber to improve its mechanical properties. The cross-linked network properties were analysed by the Flory–Rehner model and Mooney–Rivlin plots, and it was found that the long chains in the sparsely cross-linked domains of the network favoured high elongation at break and the short chains in the densely cross-linked domains contributed to high modulus, which could satisfy the functions of reinforcing and toughening the rubber materials at the same time. It was also found by analysing the filler network and aggregate morphology that the inhomogeneous cross-linked network led to an improvement in the dispersion of silica in the rubber and a significant improvement in the mechanical properties of silicone rubber.