To improve the algorithmic dimension, critical thinking, and problem-solving ability of computational thinking (CT) in students' programming courses, first, a programming teaching model is constructed based on the scratch modular programming course. Secondly, the design process of the teaching model and the problem-solving model of visual programming are studied. Finally, a deep learning (DL) evaluation model is constructed, and the effectiveness of the designed teaching model is analyzed and evaluated. The T-test result of paired samples of CT is t = −2.08, P < 0.05. There are significant differences in the results of the two tests, and the designed teaching model can cause changes in students' CT abilities. The results reveal that the effectiveness of the teaching model based on scratch modular programming has been verified on the basis of experiments. The post-test values of the dimensions of algorithmic thinking, critical thinking, collaborative thinking, and problem-solving thinking are all higher than the pretest values, and there are individual differences. The P values are all less than 0.05, which testifies that the CT training of the designed teaching model has the algorithm dimension, critical thinking, collaborative thinking, and problem-solving ability of students' CT. The post-test values of cognitive load are all lower than the pretest values, indicating that the model has a certain positive effect on reducing cognitive load, and there is a significant difference between the pretest and post-test. In the dimension of creative thinking, the P value is 0.218, and there is no obvious difference in the dimensions of creativity and self-efficacy. It can be found from the DL evaluation that the average value of the DL knowledge and skills dimensions is greater than 3.5, and college students can reach a certain standard level in terms of knowledge and skills. The mean value of the process and method dimensions is about 3.1, and the mean value of the emotional attitudes and values is 2.77. The process and method, as well as emotional attitude and values, need to be strengthened. The DL level of college students is relatively low, and it is necessary to improve their DL level from the perspective of knowledge and skills, processes and methods, emotional attitudes and values. This research makes up for the shortcomings of traditional programming and design software to a certain extent. It has a certain reference value for researchers and teachers to carry out programming teaching practice.