Most of studies on interoperability of systems integration focus on technical and semantic levels, but hardly extend investigations on pragmatic level. Our past work has addressed pragmatic interoperability, which is concerned with the relationship between signs and the potential behaviour and intention of responsible agents. We also define the pragmatic interoperability as a level concerning with the aggregation and optimisation of various business processes for achieving intended purposes of different information systems. This paper, as the extension of our previous research, is to propose an assessment method for measuring pragmatic interoperability of information systems. We firstly propose interoperability analysis framework, which is based on the concept of semiosis. We then develop pragmatic interoperability assessment process from two dimensions including six aspects (informal, formal, technical, substantive, communication, and control). We finally illustrate the assessment process in an example.