In order to solve the special complexity of architecture design of cross-domain operational systems, a design method of multi-dimensional architecture is proposed, including the design of conceptual architecture, physical architecture and logical architecture. The definitions and design procedures of the three above architectures are provided, with the conceptual architecture design including threat situation research, opposition research, capacity requirements analysis and operational concept generation, the physical architecture design including component elements selection, connection relationships description and deployment design, the logical architecture design including organizational hierarchy relationships design, operational process design, information sharing design and precision information transmission analysis. The proposed method can provide guidance for the architecture design of cross-domain operational systems.