Determination of molecular structures of organic-inorganic hybrid perovskite (OIHP) nanocrystals at the single-nanocrystal and ensemble levels is essential to understanding the mechanisms responsible for their size-dependent optoelectronic properties and the nanocrystal assembling process, but its detection is still a bit challenging. In this study, we demonstrate that femtosecond sum frequency generation (SFG) vibrational spectroscopy can provide a highly sensitive tool for probing the molecular structures of nanocrystals with a size comparable to the Bohr diameter (∼10 nm) at the single-nanocrystal level. The SFG signals are monitored using the spectral features of the phenyl group in (R-MBA)PbBr3 and (R-MBA)2PbI4 nanocrystals (MBA: methyl-benzyl-ammonium). It is found that the SFG spectra exhibit a strong resonant peak at 3067±3 cm−1 (ν2 mode) and a weak shoulder peak at 3045±4 cm−1 (ν7a mode) at the ensemble level, whereas a peak of the ν2 mode and a peak at 3025±3 cm−1 (ν20b mode) at the single-nanocrystal level. The nanocrystals at the single-nanocrystal level tend to lie down on the surface, but stand up as the ensemble number and the averaged sizes increase. This finding may provide valuable information on the structural origins for size-dependent photo-physical properties and photoluminescence blinking dynamics in nanocrystals.