We present a semi-custom design methodology based on transistor tuning to optimize the design performance.Compared with other transistor tuning approaches, our tuning process takes the cross-talk effect into account and prominently reduces the complexity for circuit simulation and analysis by decomposing the circuit network utilizing graph theory. Furthermore,the incremental placement and routing for the corresponding transistor tuning in conventional approaches is not required in our methodology, which might induce timing graph variation and additional iterations for design convergence. This methodology combines the flexible automated circuit tuning and physical design tools to provide more opportunities for design optimization throughout the design cycle.