The suicide of college students had been a social topic attracting people's attention, and the generation of suicidal ideation was an inevitable link in the psychological process of suicidal behavior. It was the focus of many researches whether the pressure of college students with suicidal ideation can be detected and relieved in time. The study aimed to analyze the therapeutic effect of cognitive behaviour therapy on psychological stress, depression, and other negative emotions of college students with suicide ideation. 114 people from 1,158 college students with suicide ideation in the Wuhan area were divided into an experimental group and a control group in this study. Students in the experimental group were given with the cognitive behaviour therapy, and students in the control group were not intervened in any way. The suicide ideation scale (despair, optimism, and sleep), psychological stress test rating, and self-reporting inventory (somatization, compulsion, interpersonal relationship, depression, anxiety, hostility, terror, delusion, and psychosis) were used to evaluate the objects in the pre-test stage, intermediate-test stage, and the tracking-test stage. The multivariate logistic regression was adopted to analyze the influencing factors of the suicide ideation of the college student. The suicide ideation of the college student was significantly positively correlated with the psychological stress, depression, interpersonal sensitivity, anxiety, and psychosis (P > 0.05); the total score of suicide ideation, despair, optimism, and sleep in the experimental group were lower than those in the control group (P < 0.05) in the intermediate-test stage and the tracking-test stage (P < 0.05); the psychological stress, depression, and anxiety of the college students in the experimental group in the intermediate-test and tracking-test stage were slighter than those in the control group (P < 0.05); the somatization, compulsion, and interpersonal relationship of students in the experimental group were significantly lower than those in the control group (P < 0.05). The psychological stress, depression, interpersonal sensitivity, anxiety, and psychosis were all risk factors for the college student to have suicide ideation. Negative emotions such as psychological stress, emotional depression, and anxiety of the college student with suicide ideation could be improved effectively by cognitive behaviour therapy, and the level of suicide ideation could be reduced finally.