In order to increase the protein content of snack cracker, different levels of cottonseed flour (CSF: 0, 10, 20, 30 g/100 g) and enzyme (Crackerase: 0, 0.02, 0.05 g/100 g) were added to cracker formula. The analysis of solvent retention capacity (SRC) found the lactic acid-SRC value of flours decreased, while water, sucrose, Na2CO3-SRC values increased with the increasing level of CSF. Alveograph results indicated CSF addition increased the tenacity and decreased the extensibility of dough. Enzyme addition decreased the tenacity and extensibility of dough. Mixolab analysis found that CSF addition increased the development time and mixing stability of dough, but resulted in lower peak viscosity and retrogradation degree of starch. At the same time, all the Mixolab parameters decreased after enzyme addition. Baking performance results indicated that CSF addition decreased the cracker breaking force and stack height, while enzyme addition increased the cracker stack height and decreased its breaking force. Sensory evaluation showed that high acceptability crackers could be produced at 20, 30 g/100 g CSF and 0.05 g/100 g enzyme addition levels. The results obtained in present study can give scientific and useful knowledge for food industry to produce nutritional crackers with high protein content.