Live-streaming, with real-time classroom interaction, is gaining traction in distance learning, yet its use in rural inquiry-based science education remains underexplored. This study, thereby, adopted the “P-D/O-Q/D-E-T inquiry” approach (Hong et al., 2024) for rural students (i.e., Predict the results of the experiment; Do an experiment; Observe what happens with the experiment; Quiz on the reasons for students to Discuss and argue; Explanation of the science phenomenon by teachers; and Transform the science phenomenon to other occasions – by students), and explored how their learning cognitive and emotional processes related to their learning progress. A single-group quasi-experimental study and a science unit, Buoyancy, were implemented. Ten rural primary schools were invited to participate in the live-stream lessons and respond to questionnaires, with groups of 5–8 students from each school. The survey received 69 valid responses to proceed with structural equation modeling. Students’ attitudes toward scientific inquiry showed a positive correlation with their engagement in learning and immersive experiences, which contributed to their learning progress. However, the predictive power between flow experience and learning progress was higher than that of learning interest to learning progress, indicating that the cognitive process is more crucial than the affective process in live-stream inquiry-based education of science. This study advocates that the integration of the P-D/O-Q/D-E-T experiential investigative learning model within a live-broadcasting setting can offer a unique approach to handling limited resources for rural students to participate in natural science learning.