Nanoscale molybdenum oxide (nano‐MoO3) is widely used in industrial and environmental fields and its release to the environment is increasing. However, the potential effect of nano‐MoO3 on rice (Oryza sativa L.) seedling growth is unclear. Herein, the different impacts of vaired concentrations (0, 50, 100, 200 and 300 μg Mo L–1) of Na2MoO4 and nano‐MoO3 on the growth and nitrate (NO3–) utilisation of rice were investigated using hydroponics. The Mo concentration in roots and shoots, N metabolism enzyme activity, root morphology, root redox ability and root exudates were then analysed to understand the potential mechanisms of the growth impacts. Results showed that the Mo concentration in rice roots increased incrementally as the amount of Mo application increased, whereas different Mo sources did not affect the Mo concentration in shoots. Both Na2MoO4 and nano‐MoO3 promoted the growth and NO3– utilisation of rice. The promotion effects of higher nano‐MoO3 dosages were better than those of Na2MoO4. Nano‐MoO3 application significantly affected the activity of nitrate reductase (NR), glutamine synthetase (GS) and glutamate synthase (NADH‐GOGAT), which in turn promoted NO3– assimilation. Additionally, rice seedlings treated with nano‐MoO3 had a relatively high rice root volume, surface area, total absorption area, active absorption area, low‐molecular‐weight organic acids, root oxidation and reduction capacities. Based on these results, it is proposed that nano‐MoO3 facilitates rice growth and NO3– assimilation via the enhancement of nitrogen metabolism enzyme activity and the promotion of good root morphological and physiological characters with high root secretion concentration and redox ability. This study provides insights regarding the further application of nano‐MoO3 in agriculture enhancing N use efficiency and rice productivity.