The blended synchronous classroom fosters equitable and balanced educational development; however, challenges persist, including low motivation and suboptimal effects on the deep learning of remote students. This study employs a student-centered learning approach and incorporates the process-oriented guided inquiry learning (POGIL) strategy into the blended synchronous science classroom. In this study, 182 fourth-grade students from four primary classes in south China were allocated using a quasi-experimental approach; among these four classes, one class from the urban area (proximal end) and one from the remote area (remote end) were paired, forming two matched classes, which constituted experimental group and control group. The experimental group took POGIL instruction, while the control group took traditional synchronous classroom instruction. The results indicated that students in classes using the POGIL intervention scored significantly higher than those in non-POGIL classes and that the POGIL instructional intervention not only facilitated the learning of science knowledge of the remote students but also promoted proximal students' learning of science knowledge. In terms of deep learning, remote students in the POGIL class demonstrated significantly higher abilities in problem-solving, collaboration, communication, autonomous learning, self-efficacy, and perseverance in learning. Students expressed satisfaction with this instructional strategy. This paper discusses the effectiveness of applying the POGIL instructional strategy in teaching and technology support in the blended synchronous science classroom.