With the advancement of educational informatization, the integration of English subject and computer science has become an effective way to improve primary school students’ comprehensive English application ability and interdisciplinary literacy. The purpose of this article is to explore the practice and challenges of integrated teaching of English and computer science in primary schools under the framework of CLIL (Content and Language Integrated Learning). In this article, BPNN (Back Propagation Neural Network) model is used to quantitatively analyze the application effect of CLIL instructional mode in ELT (English Language Teaching) in primary schools. By collecting the teaching data under the traditional instructional mode and CLIL instructional mode, this article compares the differences of students’ English scores, classroom participation, language ability, intercultural communication ability and learning interest. The results show that CLIL instructional mode shows advantages in improving students’ abilities in all aspects, especially in improving students’ English scores and intercultural communication ability. This model also stimulates students’ interest in learning and promotes their comprehensive development. The integrated teaching of English and computer science in primary schools under the CLIL framework is an effective instructional mode, but it also faces some challenges. In the future, we should fully consider these challenges and take measures to deal with them.