It is an urgently problem to be solved that how to test a weapon system-of-systems capabilities in a joint operational context. Firstly, based on the capability assessment of weapon system-of-systems, a procedure of weapon system-of-systems capabilities evaluation strategies design space is proposed. Secondly, supported by agent-based simulation tools, an exploratory analysis example is given which uses the fractional factorial design and stepwise regression fit. This paper makes a better try on the measures selected of the system-of-systems capabilities in the early period of weapon equipment acquisition.