The cross-domain unmanned swarm system includes multiple unmanned platforms that can perform complex and diverse tasks, which command and control system design covers multiple technical directions, with complex and variable requirements. Traditional design methods are difficult to meet the design requirements of cross-domain unmanned swarm command and control. To solve the above problems, a command and control software design technology based on MBSE is proposed. This technology is based on Harmony methodology. In terms of requirements analysis, it analyzes the software requirements in combination with the requirements diagram of SysML. In terms of system design, it designs the system structure and system functions in combination with the block definition diagram of SysML. In terms of system verification, it describes the task flow with the activity diagram of SysML in combination with specific combat scenarios. The test results indicate that the software has a certain degree of autonomous decision-making ability, which verifies that the software itself can meet practical needs. This software design technology has strong scalability and can quickly change requirements during the design process. The designed software has strong robustness and can meet the command and control requirements of cross-domain unmanned swarm systems. It has reference significance for research in related fields.