Soft elastomers with their ability to integrate strain-adaptive stiffening and coloration have recently received significant research attention for application in artificial muscle and active camouflage. However, there is a lack of theoretical understanding of their complex molecular dynamics and mechanochromic coupling/decoupling. In this study, a topological dynamics model is proposed to understand the anchoring-mediated topology signature of self-assembled elastomers. Based on the constrained molecular junction model, a free-energy function is firstly formulated to describe the working principles of strain-adaptive stiffening and coloration in the self-assembled elastomer. A coupled ternary “rock-paper-scissors” model is proposed to describe the topological dynamics of self-assembly, mechanochromic coupling and mechanoresponsive stiffening of the self-assembled elastomers, in which there are three fractal geometry components in the topology network. Finally, the proposed models are verified using the experimental results reported in the literature. This study provides a fundamental approach to understand the working mechanism and topological dynamics in the self-assembled elastomers, with molecularly encoded stiffening and coloration.