This study aims to explore the impact of an augmented reality (AR) scientific inquiry tool based on a brain-computer interface (BCI) on students' scientific performance, flow experience, self-efficacy, and cognitive load of primary school students. The BCI-based AR inquiring tool provides real-time attention feedback to students' activities in an AR science learning environment. Before the formal experiment, a pilot study was conducted to prove that the attention estimation algorithm involved in the tool is effective and the AR learning environment based on the BCI technology is feasible. In the formal study, quantitative and qualitative data were analyzed. A total of 41 primary school students were randomly assigned to the experimental group (EG) or the control group (CG) to learn the lever principle. The students of EG used the BCI-based AR inquiring tool, and the CG used simple AR inquiring tools without real-time attention feedback. Results show that the BCI-based AR inquiring tool positively impacts students' scientific inquiry. It significantly helps students improve their science learning performance, achieve mental flow, and promote their scientific inquiry participation self-efficacy. Besides, no significant effect on cognitive load was found. The interview results indicate that students have a positive attitude toward the BCI-based AR scientific inquiry tool.