SummaryPea proteins has been widely used in food industry due to its functionality and health benefits. Pea peptides derived from pea proteins are considered as promising source of novel functional food. However, the chemical structure of pea peptides with immunomodulatory activity remains unclear. In this work, 46 pea peptides with molecular weight from 533.28 to 1462.78 were identified from pea protein hydrolysates. The hydrolysates could significantly increase the immunomodulatory activity of the macrophages by elevation of phagocytic activity, promoting the production of nitric oxide and pro‐inflammatory cytokines (TNF‐α and IL‐6) at the doses of 0.25–1.0 mg mL−1. Moreover, upregulation of iNOS, TNF‐α and IL‐6 were related to the activity of pea protein hydrolysates. Fourteen peptides with activity scores > 0.3 showed good affinity with TLR4/MD‐2 by molecular docking. TLR4 activation was involved in the immunomodulatory activity of bioactive pea peptides through a hydrogen bond, Pi‐cation, Pi‐Sigma, Pi‐Pi stacked and/or Pi‐Pi T‐shaped interactions respectively. The above results indicated that pea peptides could be used as healthy food with immunomodulatory function, promoting the development of pea proteins in the functional food industry.