“Computational thinking” has been an important indicator for evaluating students’ high-order thinking in K-12 education in recent years. It has common thinking modes with mathematics thinking in many fields such as problem-solving. Therefore, developing computational thinking in mathematics has become a global trend. A three-layer “PBL+CT” theoretical model in primary school mathematics to develop students’ computational thinking is built. In the model, the content layer is PISA-oriented and drives teaching through the problem, the teaching layer is the mathematical model of non-programming plugged that integrates with computational thinking elements and constructs the problem-solving teaching procedure, and the goal layer is of computational thinking in relevant to the six core skills of decomposition, abstraction, algorithmic thinking, critical thinking, problem-solving, and collaborative learning. The course *How to Enclose the Largest Area* in primary mathematics was taken as an example, specific teaching designs and implementations in terms of the theoretical model were conducted, and the effectiveness of the model was verified in this research. Classroom observations, questionnaires, self-assessments, and interviews were used to verify the effectiveness of the model in promoting the development of computational thinking in primary students. It is found that the “PBL+CT” teaching model in primary school mathematics can significantly cultivate students’ computational thinking, especially in the fields of decomposition, algorithmic thinking, and collaborative learning. Based on the results, the research further summarizes and reflects on the mathematics teaching of “PBL+CT” to promote the development of students’ computational thinking in primary school.