Guided waves structural health monitoring (SHM) has been widely and deeply investigated at home and abroad. The development of integrated software and hardware for guided waves SHM system is very important for the engineering application of this technology. In this paper, a software data management module of the guided waves SHM system is designed based on the LabVIEW virtual instrument platform，aiming at the problems of a lot of data types、large amount of data、lacking standardized treatment. This paper proposed the whole structure of the data management module and developed functional subunits in data management module, including data interface layer, function driver layer and application interface layer. Finally, the module program interface is designed and the functional subunits are implemented. The experiments on the composite wing box and a series of tests on software performance are carried out, showing that the file management module can meet the requirements of all functions. Additionally, the software module is suitable for structural health monitoring engineering.