Zinc phthalocyanine carrying sulfenyl and 6-sulfydryl linkers was firstly used to functionalize with sulfur vacancies MoS2. The synthesized MoS2/ZnPc composite was further prepared to be PVA (polyvinyl alcohol) thin films by a drop coating method. The microscopic structures and photophysical properties of novel MoS2/ZnPc composite were characterized. A series of analysis results indicate that zinc phthalocyanine with sulfenyl and 6-sulfydryl linkers is loaded to sulfur vacancies of MoS2 by ligand conjugation. The third order nonlinear optical properties of MoS2/ZnPc composite were studied by an open aperture Z-scan technique at 532 nm with 4 ns laser pulses width. In comparison with individual MoS2 or ZnPc, whether MoS2/ZnPc solution or MoS2/ZnPc/PVA film sample possesses larger third order nonlinear absorption coefficients (β) and lower limiting thresholds (F50). It can be ascribed to a combination of different NLO absorption mechanisms for MoS2/ZnPc composite, including one-photon absorption, two photon absorptions and nonlinear scattering of MoS2, triplet excited state absorption of ZnPc, nonlinear scattering of MoS2/ZnPc and the photo-induced electron transfer or energy transfer (PET/ET) process between MoS2 and ZnPc moieties.