The management process of the new cyber-physical systems (CPPS) development is a complex task that requires the combination of physical and cybernetic components. Now there are no architectural solutions and approaches that allow to automate the management process of CPPS development based on the" end-to-end development" concepts, which will reduce the time and development cost. This article proposes a method for functioning algorithms synthesis. As a result of manipulations, the developer can get many options for algorithms synthesis into one, and the most optimal, according to the requirements that need to be achieved. This method can be implemented as a software in the form of an automation system for the CPPS development control process.