Formamidinium lead triiodide (FAPbI3) perovskite quantum dots (PQDs) show great advantages in photovoltaic applications due to their ideal bandgap energy, high stability and solution processability. The anti-solvent used for the post-treatment of FAPbI3 PQD solid films significantly affects the surface chemistry of the PQDs, and thus the vacancies caused by surface ligand removal inhibit the optoelectronic properties and stability of PQDs. Here, we study the effects of different anti-solvents with different polarities on FAPbI3 PQDs and select a series of organic molecules for surface passivation of PQDs. The results show that methyl acetate could effectively remove surface ligands from the PQD surface without destroying its crystal structure during the post-treatment. The benzamidine hydrochloride (PhFACl) applied as short ligands of PQDs during the post-treatment could fill the A-site and X-site vacancies of PQDs and thus improve the electronic coupling of PQDs. Finally, the PhFACl-based PQD solar cell (PQDSC) achieves a power conversion efficiency of 6.4%, compared to that of 4.63% for the conventional PQDSC. This work provides a reference for insights into the surface passivation of PQDs and the improvement in device performance of PQDSCs.