Various space missions, including the Russian and Chinese interplanetary exploration collaboration in 2011 and the Phobos-Grunt space project to be relaunched by the Chinese in 2025, carry a soil preparation system (SOPSYS), which is an instrument used for scientific experiments. The design and manufacture of this precision instrument require stringent manufacturing processes and workflow of the highest quality, with every process in the project carefully monitored and controlled. All processes should be completed within the deadline so that the space project can be launched at the scheduled time. The colored Petri net (CPN) modeling method can describe a variety of resource types and execution logic, and it can be formally verified. Based on these advantages, we clearly describe the complex structure of the SPOSYS unit production process. In addition, we use critical time and the 6 sigma system to evaluate the availability and reliability of workflows, and we use elimination and simplification (ECRS) methods and constraint theory to improve the manufacturing process of the SOPSYS unit. We further provide optimization theories, methods, and insights for workflow management in time-sensitive and independent manufacturing systems.