Objective To investigate the variations of blood biochemical and physiological characteristics in the process of breeding inbred diabetic Mongolian gerbils. Methods A total of 17 blood biochemical and 22 physiological indexes of blood samples from F9 to F14 progenies were tested using an automatic biochemical analyzer and automatic blood cell analyzer. Results The results showed that uric acid (URIC), lactate dehydrogenase (LD), creatine kinase (CK), amylase (AMY), glucose (GLU), percentage of mononuclear cells (MON%), mean corpuscular hemoglobin content (MCH), mean corpuscular hemoglobin concentration (MCHC), and mean platelet volume (MPV) increased with an increasing number of generations. Meanwhile, cholesterol ( CHOL), eosinophil direct count ( EOS), percentage of eosinophils ( EOS%), red blood cells ( RBC), hematocrit ( HCT), and hemoglobin ( HGB) decreased with the generations. The levels of albumin (ALB), total protein (TP), triglyceride (TG), high?density lipoprotein (HDL), urea nitrogen (BUN), total bilirubin (TBIL), creatinine (CRE), alkaline phosphatase (ALP), aspartate aminotransferase (AST), and the other indexes remained stable. Conclusions The blood biochemical and physiological indexes vary across the generations in the process of inbreeding diabetic gerbils, especially for those indexes related to glucose and lipid metabolism, which are indicators of the pathogenic characteristics of diabetes. The findings also imply that selective inbreeding exerts an influence on the animals’ biological characteristics.