Traditional instruction of science knowledge may lead to low motivation in science learning. Science inquiry may improve students' science concept knowledge and insights about science. However, the teaching of science inquiry is a complex process which involves multiple inquiry steps. Therefore, this study designed an inquiry map system for supporting inquiry-based instruction, and investigates the impact of the use of inquiry map system in teaching on students' conceptions of learning science. Participants were 49 junior eighth-grade students from two classes randomly one of which was assigned as experimental group (N=25) teaching with inquiry map, while the other one as control group (N=24) lectured in traditional instruction. Data collection including the questionnaires and learning test were analyzed with ANCOVA. The results showed that the use of the inquiry map system in teaching reduced students' conception of ‘memorizing', and' calculating and practicing', and enhanced the extent of ‘seeing in a new way', ‘deep motivation', and ‘deep strategy' in learning sciences.