The study compared and analyzed the quality of loquat jam with different cooking times through physicochemical parameters, headspace-gas chromatography-ion migration spectroscopy (HS-GC-IMS) and intelligent senses. The results showed that with the prolongation of the cooking time, the color of loquat jam slowly deepened, the energy significantly increased, the adhesiveness, gumminess, hardness and chewiness enhanced, the free amino acid content increased from 22.40 to 65.18 mg/g. The organic acid content increased from 1.64 to 9.82 mg/g. Forty-seven volatile flavor compounds were identified in five types of loquat jam using HS-GC-IMS, among which the relative content of aldehydes was sharply higher than that of other chemical substances, playing an important role in the flavor formation of loquat jam. LJ0, LJ1 and LJ2 had higher aldehyde content, followed by LJ3 and LJ4 had the lowest aldehyde content. The orthogonal partial least squares-discriminant analysis (OPLS-DA) screened 15 marker compounds that could distinguish five types of loquat jam. The E-nose results showed a significant difference in olfactory sense between loquat jam cooked for 100 and 120 min. The E-tongue results corroborated the results of free amino acids (FAAs) and organic acids, indicating that the gustatory sense of loquat jam changed significantly when the cooking time reached 120 min. The results provided a basis for further research on the relationship between the cooking process and quality characteristics of loquat jam.