<p>The blended synchronous learning environment (BSLE) has been utilized to promote educational equity. However, low engagement among remote students remains a significant challenge. While numerous studies have confirmed that inquiry-based learning (IBL) can enhance student engagement, its effectiveness in the BSLE context has not yet been empirically validated. This study examined the impact of IBL in the BSLE on primary school students’ engagement and learning performance, focusing on collaborative problem-solving ability and science process skills, which have been proven to be enhanced by IBL. A quasi-experiment was conducted with 159 fourth-grade students from two schools in South China, pairing one onsite (urban) and one remote (rural) class into experimental (IBL intervention) and control (traditional experimental teaching method) groups. Results indicated that IBL was associated with significant improvements in student engagement, collaborative problem-solving ability and science process skills for both remote and onsite students. Specifically, rural students showed significant improvements in the affective dimension of student engagement and in the first two levels of collaborative problem-solving ability. Onsite students demonstrated superior performance in each of their sub-dimensions. Notably, while there were no significant differences in student engagement and collaborative problem-solving ability between remote and onsite students, urban students performed significantly better than rural students in science process skills. This study suggests that IBL may support relative educational equity through engaging both urban and rural students in science activities, while helping rural students develop higher-order abilities such as collaborative problem-solving abilities and science process skills. However, further empirical validation in broader regions and populations is required.</p>