The all-round penetration of artificial intelligence technology has brought about a drastic change in the educational landscape, and the teaching system of colleges and universities relies on artificial intelligence technology to expand its own boundaries, leading to interdisciplinary knowledge fusion between dual colleges and universities. With the support of AI technology, a teaching system design idea of interdisciplinary knowledge integration is proposed, and a teaching innovation system of interdisciplinary knowledge integration between dual colleges and universities is established. Taking the learners’ interdisciplinary knowledge point response situation as an entry point, input modeling is carried out for the learners’ interdisciplinary knowledge points, forgetting coefficient, etc., and the dual colleges’ interdisciplinary knowledge tracking SA-BiGRU model is established by combining BiGRU and the attention mechanism, and simulation verification is carried out to verify its effectiveness. Taking a vocational college in province G as an example, a dual college interdisciplinary teaching comparison experiment was designed in combination with the teaching innovation system, so as to verify the effectiveness of the interdisciplinary knowledge integration teaching innovation system. The results show that the AUC and ACC of the SA-BiGRU model can reach up to 0.837 and 0.841 respectively in interdisciplinary knowledge tracking, and the learners’ interdisciplinary knowledge reserve and ideological literacy level have been improved by 1.36 and 1.82 points respectively compared with that before the experiment. Relying on artificial intelligence technology can promote interdisciplinary knowledge integration, provide a new research direction for the development of interdisciplinary intelligence in BiGR, and lay the foundation for the cultivation of highly skilled and qualified applied talents.