Objective. To investigate the pathogenesis of allergic asthma via the nanoliter two-dimensional liquid chromatography (nano-2D-LC) technique. Method. 24 Wistar rats were randomized into 3 groups: the blank-control group (A), the restrained group (B), and the asthma model group (C). The nanoliter two-dimensional liquid chromatography (nano-2D-LC) technique was used to study the differential protein expressions of the serum in asthmatic rats. Results. Compared with the restrained group, the data from the asthma model group displayed a distinctive peak, that is, peak number 13 (94.731 min). The data also displayed three missing peaks in the asthma group, that is, peak number 1 (77.489 min), peak number 2 (78.418 min), and peak number 5 (80.533 min), suggesting that the corresponding peptides might be related to the pathogenesis of asthma. Compared with the blank-control group, the restrained group showed 4 new peaks, that is, peak number 2 (78.418 min), peak number 4 (79.398 min), peak number 5 (80.533 min), and peak number 7 (81.824 min). The restrained group also displayed a missing peak, that is, peak number 3 (78.804 min), indicating that those 5 polypeptides might be related to the binding-induced stress stimuli. Conclusion. The study suggests that the pathogenesis of allergic asthma is closely related to abnormal levels of proteins; however, future animal experiments should identify the specific protein expressions caused by stress factors.