In this work, by coupling scanning Kelvin probe force microscopy (SKPM) and photoconductive atomic force microscopy (pcAFM), the variation of the surface potential, photogenerated voltage, and photocurrent networks of the perovskite solar cells (PSCs) with different film topography is studied. The nanoscale photovoltaic reaction of different perovskite capping layers with three different perovskite crystalline sizes is first studied by using the SKPM technique. The performance of the overall device is correlated with the local nanostructure of the perovskite film. Photocurrent maps under various applied voltages are also presented. The pcAFM measurements on three different morphology positions determine that the defect region on the capping layer can induce the charge recombination process in the complete PSCs and thus suppress the V-oc in the complete device. These results suggest that the performance of PSCs can still be improved through better control of morphology. Henceforth, SKPM coupled with pcAFM techniques has the potential to become a routine characterization tool for perovskite organic and hybrid photovoltaics.