The stability control of the overlapped tunnels system has been one of the hot issues and difficulties in tunnel and underground engineering field. According to the whole process analysis for instability evolution of the overlapped tunnels, its nonlinear dynamics characteristics are studied by the nonlinear dynamics method, including material and energy metabolism, fluctuation, thermodynamics irreversible process, correlation dimension and entropy. On this basis, combining with stability control measures such as grouting, bolt and gunite and so on, the dynamics mechanism and energy dissipation mechanism for stability control of the overlapped tunnels system are studied by synergetics and dissipative structure theory. The nonlinear dynamics evolution law of the control process is also revealed. This research is not only able to provide theoretical support for establishing optimal control model and risk control principle based the nonlinear dynamics, but also of great significance for the stability control technology of the overlapped tunnels.