High energy resolution energy-loss near-edge structures (ELNES) at the carbon K-edge of copper phthalocyanine (CuPc) and its chlorinated molecular crystals were observed using electron energy-loss spectroscopy combined with a scanning transmission electron microscope equipped with a monochromator. The ELNES spectra were investigated using first-principles band structure calculations with a core-hole introduced into the Is orbitals of the nonequivalent C atoms. The calculated spectra including half a core-hole were consistent with the experimental spectra. The spectral features could be interpreted in terms of the different contributions of the partial density of states (PDOS) of nonequivalent C atoms with different transition energies depending on the site. The core-hole effects were also discussed using the spatial distribution of unoccupied states and PDOSs, which revealed site-dependent core-hole effects, where a C atom with a strong spatial distribution intensity of the unoccupied states in the ground state (GS) are susceptible to the core-hole effects. The spectral changes due to chlorination of the CuPc molecule were mainly attributed to an increase of the threshold energy of the C atoms bonded to chlorine, and the influence of the change in the PDOS by chlorination was not significantly large.