Colored traveling salesman problem (CTSP) can be applied to Multi-machine Engineering Systems (MES) in industry, colored balanced traveling salesman problem (CBTSP) is a variant of CTSP, which can be used to model the optimization problems with partially overlapped workspace such as the planning optimization (For example, process planning, assembly planning, productions scheduling). The traditional algorithms have been used to solve CBTSP, however, they are limited both in solution quality and solving speed, and the scale of CBTSP is also restricted. Moreover, the traditional algorithms still have the problems such as lacking theoretical support of mathematical physics. In order to improve these, this paper proposes a novel hybrid genetic algorithm (NHGA) based on Wiener process (ITÖ process) and generating neighborhood solution (GNS) to solve multi-scale CBTSP problem. NHGA firstly uses dual-chromosome coding to construct the solutions of CBTSP, then they are updated by the crossover operator, mutation operator and GNS. The crossover length of the crossover operator and the city number of the mutation operator are controlled by activity intensity based on ITÖ process, while the city keeping probability of GNS can be learned or obtained by Wiener process. The experiments show that NHGA can demonstrate an improvement over the state-of-art algorithms for multi-scale CBTSP in term of solution quality.