Crayfish, Procambarus clarkia, is an important freshwater aquaculture species in China. Nonetheless, with this rapid development of the aquaculture industry, crayfish diseases have emerged as an increasing problem in recent years, with outbreaks of various viral and bacterial diseases causing huge economic losses. The occurrence of diseases in shrimp is related to pathogenic infection, environmental degradation, nutrition disorders, and a decrease in self-immunity. Different pathogenic factors have different effects on the physiological metabolism of shrimp, which are reflected by changes in immunity, metabolism, and physiological and biochemical indicators. Establishing these disease-associated indicators will provide a helpful tool to rapidly identify shrimp infections and establish the major harmful factors of multi-pathogenic infections. To screen for the serological markers, physiological markers, and biochemical indices of diseased P. clarkia and provide a basis for disease risk assessment in shrimp culture, a virulent pathogenic bacterial strain, Aeromonas hydrophila, was injected into P. clarkia at a dose of 1 LD₅₀. A total of 23 indices, including non-specific immunity, carbohydrate metabolism, lipid metabolism, protein metabolism, and physiological and biochemical indices, were analyzed in the serum at the early stage of infection (12 h), onset (24–72 h), and post-infection recovery (90 h) periods. The results showed that among the eight non-specific immune indices in the onset period, catalase (CAT) activity and total antioxidant capacity (T-AOC) were significantly higher in the infection group (P＜0.01), with mean values 3.29 and 2.56 times higher than those of the control group, respectively. The concentrations of albumin (ALB) and urea (UREA) were significantly higher in the infected group during the diseased period (P＜0.01), with average concentrations 1.75 and 5.58 times higher than those in the control group, respectively. The activity of amylase (AMY) was significantly lower in the onset period (P＜0.01), with a 3.87 times lower activity than that in the control group. Activities of the enzymes creatine kinase (CK), alanine aminotransferase (ALT), glutamate aminotransferase (AST), and glutathione peroxidase (GSH-Px) were significantly higher in the onset period (P＜0.01), with activities 16.72, 219.21, 74.43, and 2.66 times higher than those in the control group, respectively. Among the detected indices, glucose (GLU), triglycerides (TG), total protein (TP), and lipase (LPS) did not change significantly (P＞0.05). These results indicated that changes in the CAT, T-AOC, ALB, UREA, AMY, CK, ALT, AST, and GSH-Px indices in the serum of P. clarkia were extremely indicative of disease onset caused by bacterial infection. The results of this study could, ultimately, provide a novel technical basis for disease risk assessment and allow early warning of disease in crayfish aquaculture.