To efficiently analyze the electromagnetic scattering from composite perfect electric conductor (PEC)-dielectric objects with coexisting closed-open PEC junctions, a modified hybrid integral equation (HIE) is established as the surface integral equation (SIE) part of the volume surface integral equation (VSIE), which employs the combined field integral equation (CFIE) and the electric field integral equation (EFIE) on the closed and open PEC surfaces, respectively. Different from the traditional HIE modeled for the objects whose closed and open PEC surfaces are strictly separate, the modified HIE can be applied to the objects containing closed-open junctions. A matrix equation is obtained by using the Galerkin’s method of moments (MoM), which is augmented with the spherical harmonics expansion-based multilevel fast multipole algorithm (SE-MLFMA), improved by the mixed-potential representation and the triangle/tetrahedron-based grouping scheme. Because in the improved SE-MLFMA, the memory usage for storing the radiation patterns of basis functions is independent of the SIE type in the VSIE, it is highly appropriate for the fast solution of the VSIE that contains the HIE. Various numerical experiments demonstrate that during the calculation of composite objects containing closed-open PEC junctions, the application of the modified HIE in the VSIE can give reliable results with fast convergence speed.