Sea cucumbers are recognized as food and drug resources with many nutritional benefits, and Apostichopus japonicus is a kind of sea cucumber with good quality.Processing methods have some effect on its quality. This study aimed to explore the effects of Apostichopus japonicus with three different processing methods (dried, instant, and enzymatic sea cucummbers) on intestinal microflora dysregulation using a cyclophosphamide (cy) induced immunosuppressive mouse model. The expression of lysozyme, immunoglobulin A (IgA), and polymeric immunoglobulin receptor (pIgR) in the intestine and gut microbiota were investigated. The results showed that three types of A. japonicus could improve mucosal immunity and regulate gut microbiota. Dietary A. japonicus could reverse microbial imbalance, including increasing the bacterial diversity, enhancing the number of Bifidobacterium, and changing the bacterial composition. The most effect was observed with dried A. japonicus. Expression of lysozyme and IgA in the intestine was significantly increased. This study identified positive effects of dietary A. japonicus on mucosal immunity, particularly on gut microbiota, suggesting that dietary A. japonicus may aid in improving mucosal immunity and preventing exogenous infection. Additionally, the processing method has some effect on immunomodulatory function.