Carboxylic acids (CAs) are important molecular markers in the study of petroleum biodegradation. This work presents a vortex-assisted liquid–liquid microextraction (VALLME) method, followed by comprehensive two-dimensional gas chromatography-mass spectrometry (GC × GC–MS) analysis for the profiling of CAs in complex oils. The designed extractant containing CAs in VALLME can be silylated immediately and injected into GC × GC–MS without any post-treatment. More than 400 individual CAs, including alkanoic acids, cyclic aliphatic acids and aromatic acids, were putatively or positively identified. With good reproducibility and high sensitivity, VALLME combined with GC × GC–MS was applied to investigate the distribution and evolution of individual CAs in crude oil during laboratory biodegradation. It was found that acyclic acids and monocyclic aliphatic/aromatic acids could be detected at all stages of oil biodegradation, while polycyclic aliphatic/aromatic acids could only be identified in oils at a relatively higher degree of biodegradation. In addition, the contents of each type of CA changed regularly during biodegradation. Targeted analysis on the distributions of individual acyclic acids showed that the abundance ratio of short chain to long chain n-alkanoic acids kept increasing during biodegradation, which might reflect the multiple origins of short chain n-alkanoic acids. Moreover, based on the distributions of pristanic/phytanic acid and pristane/phytane in oils with different biodegradation degrees, pristanic and phytanic acid seemed to be more susceptible to degradation compared to their hydrocarbon analogues, and pristane might be more susceptible to degradation in comparison to phytane.