Bactrian camel (Camelus bactrianus) is a large, even-toed ungulate native to the desert areas of Central Asia. Aggregated lymphoid nodules area (ALNA) is known as the special anatomical structure of a Bactrian camel’s stomach that is found in the cardiac glandular area of the abomasum. To advance the exploration of the mucosal immune function of this anatomical feature within the gastrointestinal tract, we quantified the expressed proteins in ALNA using iTRAQ-based proteomic analysis in 6 Bactrian camels. In the experiment, we sampled the reticular mucosal folds region (RMFR) and longitudinal mucosal folds region (LMFR) separately from the ALNA and compared their proteomic quantification results with the samples from the Peyer’s patches (PPs).