We investigated the influence of heat treatment on the crystallographic structure and ferroelectric phase transition behavior of barium titanate (BaTiO3, BT) nanocubes assembled into highly ordered monolayers, using tip-enhanced Raman spectroscopy (TERS), temperature-dependent micro-Raman spectroscopy, and scanning transmission electron microscopy (STEM). TER spectra from individual BT nanocubes with the size of about 20 nm were obtained with a side-illumination optical setup, and revealed that heat treatment enhances their tetragonality. The result of temperature-dependent micro-Raman spectroscopy showed that the ferroelectric phase transition behavior of the monolayers becomes similar to that of bulk BT through heat treatment in spite of their thickness. STEM observation for the cross-section of the heated BT nanocube monolayer showed that amorphous layers exist at the interface between BT nanocubes in face-to-face contact. These results indicate that the tetragonal crystal structure of BT nanocubes is stabilized by heat treatment and the formation of the interfacial amorphous layer during heat treatment may be a key to this phenomenon.