The purpose of this study is to explore the nutritional components and physicochemical properties in five types of protein raw materials and their mixed powder, including soybean meal, cottonseed meal, rapeseed meal, Distillers Dried Grains with Solubles (DDGS), and Clostridium autoethanogenum Protein (CAP). Key indicators were determined on the processing quality of pellet feed and energy consumption of granulation. A comprehensive evaluation was also performed on the granulation of protein raw materials. Five kinds of protein raw materials were mixed with ground corn at the weight ratio of 3:7 in a single-factor experimental design. The soybean meal was taken as the control group, whereas, the pelletized feed was prepared with the same processing parameters. Correlation analysis and Partial Least Squares regression (PLS) were conducted to compare the pelletizing quality of different protein raw materials. The results showed that there were significant differences in nutritional components and physicochemical properties of raw materials, where the CAP presented a high protein content and solubility while low fat and fiber, the cottonseed meal with high fiber, the rapeseed meal with high fiber and low protein solubility, as well as the DDGS with low protein and high fat. Water absorption of protein raw materials was ranked in descending order: CAP, soybean meal, cottonseed meal, rapeseed meal, and DDGS. The energy consumption of CAP group and cottonseed meal group was higher than other group, and soybean meal group was lowest; the higher Modified Pellet Durability Index (MPDI) of the cotton meal group and CAP group was 92.72% and 90.57% respectively, and the lowest MPDI of rapeseed group was 79.68%. The highest hardness of CAP group was 130.95 N, and the lowest hardness was 74.26 N in DDGS group. The highest gelatinization degree of CAP group was 45.56% and the lowest of gelatinization degree was 31.36% in DDGS group. The partial least squares regression model demonstrated that the protein content and solubility, as well as the water absorption significantly improved the hardness, PDI, and MPDI of pellet feed. The crude fiber content, protein solubility, and water absorption contributed tosaving the energy consumption of pelletizing. The granulation characteristics were ranked in the order from high to low: CAP, cottonseed meal, soybean meal, rapeseed meal, and DDGS. The findings can provide a sound reference for the selection of protein raw materials in the actual production of pellet feed.