To investigate the effect of intramuscular fat (IMF) on the lipids and flavor compounds of pork, high intramuscular fat (HIMF) and low intramuscular fat (LIMF) samples from 165 Duhua pigs (Duroc ♂ × Guangdong small-eared spotted pigs ♀) were analyzed for their differences in lipids and flavor compounds using ultra-high performance liquid chromatography-mass spectrometry (UPLC-MS)-based lipidomics and comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOF MS)-based flavoromics. A total of 2081 lipids were identified in both groups and categorized into 40 subclasses, with triglycerides (TG), zymosterol (ZyE), phosphatidylcholine (PC), and phosphatidylethanolamine (PE) being the major constituents. A total of 25 differentially expressed lipids were selected, including 6 TGs, 6 PEs, and 5 hexosylceramides (Hex1Cers). Flavoromics results revealed that 1649 and 1842 flavor compounds annotated with CAS numbers were identified in HIMF and LIMF, respectively. A total of 76 differential volatile flavor compounds were identified, including 19 esters, 15 organic heterocyclic compounds, 13 hydrocarbons, and 10 alcohols. Among these, eight key flavor compounds, with a relative odor activity value (ROAV) ≥ 1, were determined including 2,3-butanedione, 2-nonenal, and heptanal. The results of the omics integration indicated that the differences in flavor between HIMF and LIMF were primarily mediated by the regulatory pathway governing fruity flavor generation through lipid hydrolysis. Ethyl undecanoate and ethyl tetradecanoate showed positive correlations with multiple TGs but negative correlations with certain phospholipids (e.g., PC and PE). This study provides new insights for the improvement and development of high-quality pork in China.