The existence of hidden complex cavities formed inside a self-assembled nanocrystalline structure is discovered in real-time by using surface plasmon resonance near-field refractive index fingerprinting. Furthermore, computer analysis of the naturally occurring R-G-B interference fringes allowed us to reconstruct the 3D cavity formation and crystallization processes quantitatively. For the case of an aqueous droplet containing 10% by volume of 47 nm Al2O3 nanoparticles, the submicrometer-scale inner cavity peak grows up to 0.5% of the entire crystallized crust height of over 150 mu m. The formation of the complex inner structure was found to be attributable to multiple cavity inceptions and their competing growth during the aquatic evaporation. This outcome provides a better understanding and feasible control of the formation of nanocrystalline inner structures.