Immunoglobulin is one of the major effector factors in the adaptive immunity of fish. Thus, the study of immunoglobulin is crucial for the prevention and control of disease in fish. In this study, the complete cDNA sequence of secretory immunoglobulin Z heavy chain gene (GenBank accession no. MZ274344.1) of Carassius auratus indigentiaus was cloned by PCR and RACE. The complete cDNA sequence of C. auratus indigentiaus sIgZ heavy chain gene was 2083 bp, and its open reading frame (ORF) was 1668 bp, which encoded a peptide chain composed of 556 amino acids, with a relative molecular weight of 61.59 kD and theoretical isoelectric point of 7.03. The sIgZ heavy chain gene structure of C. auratus indigentiaus is composed of one variable region (V), four constant regions (CH1-CH4), and one secretory tail (Sec tail). According to the homologous sequence retrieval in GenBank, the similarity of sIgZ amino acid sequence between C. auratus indigentiaus and other fish was as follows: Megalobrama amblycephala (63.17%), Ctenopharyngodon idellus (60.82%), Cyprinus carpio (52.98%), Oncorhynchus mykiss (37.06%), and Sparus aurata (60.82%). Constructing a phylogenetic tree using the neighbor-joining method in MEGA 5.1, sIgZ of C. auratus indigentiaus was found to cluster into one branch with the IgZ of Cypriniformes, wherein the genetic evolution relationship between C. auratus indigentiaus and M. amblycephala was the closest. qPCR analysis revealed that C. auratus indigentiaus sIgZ gene expression was highest in the head kidney, followed by mesonephron, intestine, spleen, and gonad. After artificial infection with Aeromonas hydrophila, the C. auratus indigentiaus sIgZ mRNA levels first increased and then decreased in different tissues within 28 d. The relative expression levels of sIgZ in mucosal immune tissues (intestine and skin) peaked earlier than that in systemic immune tissue (head kidney and spleen), wherein the relative expression of sIgZ in the intestine and skin at peak was significantly higher than that in the head kidney. These results showed that sIgZ of C. auratus indigentiaus may play an important immune function in mucosal immune tissue (e.g., intestine and skin).