This study examined the change in the two groups of senior primary school students' understanding of particulate nature of matter (PNM) before and after each group involved in related instructions, namely inquiry instruction with multiple representations (IIMR) and regular instruction (RI). Data were collected through a two-tier questionnaire, and the data were analysed utilising statistical methods to compare the extent of change across the groups. The results revealed that both groups of students held similar but poor understandings of PNM before the instruction. Following the instruction, the IIMR students showed a greater improvement in scientific understandings about the PNM compared to their counterparts in the RI group. The results exhibited that carefully designed instruction of IIMR were strongly served for fostering students' scientific understanding of PNM in comparison to the RI.