The mechanism of reaction in isobutane/2-butene alkylation systems is extremely complicated, accompanied by numerous side reactions. Therefore, a comprehensive understanding of the reaction pathways in this system is essential for an in-depth discussion of the reaction mechanism and for improving the selectivity of the major products (clean fuel blend components). The alkylation of isobutane/2-butene was studied using a self-made intermittent reaction device with a metering, cooling, reaction, vacuum and analysis system. The alkylates were qualitatively and quantitatively analyzed using a capillary gas chromatography-mass spectrometry-data system (CGC-MS-DS) and capillary gas chromatography with flame ionization detection (CCGC-FID), respectively, and the precision and recovery of the quantitative analytical methods were verified. The results showed that the relative standard deviation (RSD) of the standard sample was below 0.78%, and the recoveries were from 98.53% to 102.85%. Under the specified reaction conditions, 79 volatile substances were identified from the alkylates, and the selectivity of C8 and trimethylpentanes (TMPs) reached 63.63% and 53.81%, respectively. The changes of the main chemical components in the alkylation reaction with time were tracked and analyzed, based on which reaction pathways were determined, and a complex reaction network containing the main products’ and the by-products’ generation pathway was constructed.