Bulk-boundary correspondence (BBC) of symmetry-protected topological (SPT) phases relates the nontrivial topological invariant of the bulk to the number of topologically protected boundary states. Recently, a finer classification of SPT phases in Hermitian systems has been discovered, known as subsymmetry-protected topological (sub-SPT) phases [Wang et al., Nat. Phys. 19, 992 (2023)]. In sub-SPT phases, a fraction of the boundary states is protected by the subsymmetry of the system, even when the full symmetry is broken. While the conventional topological invariant derived from the Bloch band is not applicable to describe the BBC in these systems, we propose to use the non-Bloch topological band theory to describe the BBC of sub-SPT phases. Using the concept of the generalized Brillouin zone (GBZ), where Bloch momenta are generalized to take complex values, we show that the non-Bloch band theory naturally gives rise to a non-Bloch topological invariant, establishing the BBC in both SPT and sub-SPT phases. In a one-dimensional system, we define the winding number, whose physical meaning corresponds to the reflection amplitude in the scattering matrix. Furthermore, the non-Bloch topological invariant characterizes the hidden intrinsic topology of the GBZ under translation symmetry-breaking boundary conditions. The topological phase transitions are characterized by the generalized momenta touching the GBZ, which accompanies the emergence of diabolic or band-touching points. Additionally, we discuss the BBCs in the presence of local or global full-symmetry or subsymmetry-breaking deformations.