In order to obtain new optical properties, such as quadratic nonlinear optical or electro‐optical properties, we have undertaken the orientation control of organic nanocrystals during their growth in the pore of sol–gel matrices by applying a high magnetic field, H, of 16 T. H favors the dye aggregation and improves the crystalline quality of nanocrystals by reducing the orientation freedom of molecules and clusters through their diamagnetic susceptibility. When H is not applied, the NPP (N‐(4‐nitrophenyl)‐(L)‐prolinol) nanocrystals generate a weak second harmonic generation (SHG) intensity due to self‐oriented domains of nanocrystals induced by dipole–dipole interactions. In the case of 3‐methyl‐4‐nitropyridine‐1‐oxide (POM), which exhibits a very weak dipolar moment, no SHG signal can be detected. When H is applied, the SHG intensity of NPP nanocrystals increases significantly due to the reduction of their orientational freedom and the increase of dipole–dipole interactions, thus improving the formation of oriented domains of nanocrystals.