The soft computing simulation design methodology of intelligent control system for mobile micro-nano-robots based on modeling of non-linear dissipative equations of robots motion with a minimum entropy production is described. It includes hierarchical levels for description of dynamic behavior of mobile micro-nano-robots based on laws of microphysics, quantum logic of intelligent dynamic behavior of control objects, optimal control of states and dynamic system theory of mechanical motion. The description of a thermodynamic intelligent behavior (with minimum entropy production) of control objects (robots) and their interrelations with Lyapunov stability conditions are introduced. The role of soft computing on the basis of GA with a fitness function as a minimum entropy production for intelligent control of mobile micro-nano-robots is discussed.