The applications for IEC 61499 that is standard architecture for developing the applications of distributed control and measurement in factory automation, have the connected structure of the graphical elements called BFB(basic function block), SIFB(service interface function block) and CFB(composite function block). The research on the composite function block has been regarded as important issues in implementing hierarchy, multi-functionality and simplicity of software. Nowadays many researchers have been investigated IEC61499 in the fields of the software modeling composed of basic function block and service interface function block, the transformation from IEC61131 to IEC61499 and syntactic extension of ECC of basic function block. However, work related to the mathematical modeling for IEC61499 composite function block using in designing software with hierarchical structure is still lacking. This paper presents the mathematical model for the structure and execution analysis of IEC 61499 composite function blocks by using notation of the set theory. Also a subaplication configuration algorithm is suggested for the subapplication corresponding to the composite function block. Then its effectiveness through the computation experiment of several distributed control applications is shown. The proposed model can be used effectively as a basis for analyzing a runtime environment of a software tool for designing and developing the applications.