FAMEs work as an alternative to petroleum-based diesel fuels for its low carbon footprint. However, FAMEs' qualities are constrained by the sources' fatty acid profiles. Fractionation of FAMEs can significantly change biodiesel's qualities. Compared to other fractionation methods, evaporative urea inclusion fractionation can rapidly and effectively separate the saturated FAMEs. In addition, FTIR analysis indicated the possible conjugation of host structures by unstable hydrogen bonding and oxygen bonding. Crystallite sizes and strain of urea inclusion compounds (UICs) were calculated from the XRD spectrum, influenced by FAMEs' structures and operation processes. Only the ratios of urea to FAMEs can significantly affect compositions in evaporative urea inclusion fractionation. However, UICs formation rates were influenced by all operation conditions, such as temperatures, pressures, and ratios of urea to FAMEs to solvent. The products were evaluated by the low-temperature performance, cetane number, oxidation stability, energy density, and emissions. Urea inclusion fractionation can significantly improve the low-temperature performance, the major constraint for enlarging the utilization. However, the decreased cetane number and oxidation stability indicated the possible need for antioxidants and cetane improvers after urea inclusion fractionation. Moreover, the unsaturated enriched products from urea inclusion fractionation can provide the feedstock to synthesize biochemical or biomaterials, such as carboxylic acids, polyesters, and biolubricants.