Polyunsaturated fatty acids are essential to human nutrition. Phyllanthus emblica L. seed oil serves as a source of enrichment for the preparation of polyunsaturated fatty acids by urea inclusion technique. Under optimal conditions (6 g urea per 3 mL free fatty acids, crystallization temperature of −6°C, and crystallization time of 19 h), the purity of polyunsaturated fatty acids was up to 98.47% and the yield was 71.85%. The urea-polyunsaturated fatty acids inclusion complex was analyzed using differential scanning calorimetry, Fourier-transform infrared spectroscopy, X-ray diffraction, scanning electron microscopy/energy, and dispersive X-ray spectroscopy. The results showed that polyunsaturated fatty acids can be successfully separated by urea inclusion fractionation. The filled and hollow hexagonal prisms of urea crystal were clearly observed. In addition, the macroscopic and microscopic morphology of palmitic acid-urea inclusion were studied after washing with solvents using scanning electron microscopy and X-ray diffraction analysis to understand the involvement of guest molecules in the hexagonal crystal structure. The results showed that washing with solvents could not remove all the palmitic acid in the hexagonal structure of the urea inclusion complex, and the formation of hexagonal structure needed the support of involved guest molecules.