Food processing methods may influence the health of dogs. However, previous studies have mostly been based on a comparison of several commercial dog foods with different ingredients. In this study, eighteen adult beagles of the same age and health status (assessed by routine blood tests) were used in the experiments. This study analyzed the effects of the following different processing methods: raw, pasteurized, and high temperature sterilization (HTS) made with the same ingredients and nutrients (based on dry matter) on serum parameters, apparent total-tract macronutrient digestibility, fecal microbiota and short-chain fatty acid (SCFA) content in beagle dogs. The data showed, after a test lasting 56-days, the apparent digestibility (ATTD) of protein and fat in HTS food was 91.9%, which was significantly higher (P< 0.05) than that in dry food (89.2%, P < 0.05). The serum content of triglyceride increased in beagles fed HTS food (P < 0.05), and the number of neutrophils in beagles fed raw food and pasteurized food increased significantly (P < 0.05), and the platelet count in beagles fed raw food showed an increasing trend compared with the beagles fed HTS food. Different processing methods had an impact on the intestinal microbiota and SCFA of beagles; at least 14 genera were significantly affected by the food produced using different processing methods. In particular, the abundance of Allprevotella, Escherichia-Shigella and Turicibacter, and the total acid content were lower in beagles fed the raw diet, whereas Streptococcus, Collinsella, Bacteroides and Ruminococcus gnavus were more abundant following the HTS diet, and Lactococcus showed the highest abundance in beagles fed the pasteurized diet. This study showed that dog food produced by different processing methods affected the health of adult beagles.