Thermoplastic polymers and composites are ubiquitous in the industry for their reshaping and fusing capabilities at elevated temperatures. The quality of heat-fused thermoplastic interfaces is of great concern for adhesion, coating, and welding applications, especially those between dissimilar materials. Kinetic evolution of the microstructures defines the mechanical performance of heat-fusion thermoplastic interfaces, which is studied here using polyethylene and polypropylene as an example. Key factors such as the viscosity and compatibility of polymers and the time and temperature of fusion are discussed by combining molecular-level simulations and structural-level hot-compression experiments. Inter-diffusion and entanglement of polymer chains are identified as the two elementary kinetic steps of the fusion, which dominate the control on the stiffness and strength of the interfaces, respectively. Experimental data shows that the quality of fused interfaces can be improved by reducing the viscosity and the interaction parameter. Following the same set of time-scaling relations as identified in the simulations, the two-step characteristics and their effects on the stiffness and strength are experimentally validated. Both simulation and the experiment results show that Young’s modulus of fused interfaces recovers faster than the strength that is controlled by polymer entanglement to a large extent, rather than diffusion. These findings add insights into the design of fusion processes, laying the ground for the applications of thermoplastic polymers and composites.