This study aims to develop a model for construction in a science inquiry class, explicitly focusing on the application of digital twin technology. This technology allows students to explore biological phenomena virtually, learning with virtual replicas and physical space in the context of learning biology. To develop the model, the researcher analyzed various research related to digital twin applications and performed a literature review in the context of effective teaching and learning strategy. Additionally, 22 students were recruited to assess the effect of the class to construct through the model at the affective domain. This study found that the construction model of inquiry class functions as guidance for interactive and immersive learning, enabling students to overcome the traditional limitations of time, space, and physical resources. Also, results showed that students significantly improved their affective domain in biology inquiry class. Consequently, three conclusions were drawn from this research. First, digital twin technology enhances student engagement and interaction, creating a more immersive and interactive learning environment. Second, personalized learning is facilitated, as the digital twin system allows for real-time monitoring and tailored feedback, fostering greater independence in students’ learning processes. Third, the digital twin-based class model proved feasible and effective in actual classes, with tangible improvements in students’ affective domain towards science and inquiry-based learning. Therefore, using the digital twin technology can help reduce the digital and educational divide by providing high-quality learning experiences in resource-limited settings.