To investigate the effects of nano-magnesium and ionic-magnesium on the growth, yield, and quality of aromatic rice variety Muyudao 49 in cold region, an experiment of applying different forms of magnesium fertilizer was conducted. The results showed that compared to the conventional fertilization treatment, the treatment with the addition of nano-magnesium had the highest SPAD value of leaves, dry matter accumulation, and yield from the heading stage to the maturity stage of Muyudao 49, followed by the treatment with the addition of ionic magnesium. The application of magnesium fertilizer significantly enhanced the enzyme activity of ADPG pyrophosphate synthase and soluble starch synthase throughout the grain filling process, significantly increased the enzyme activity of starch branching enzymes in the early stage of grain filling, and significantly reduced the enzyme activity of glutamine synthase in the early stage of grain filling. Additionally, the application of magnesium fertilizer significantly improved the brown rice rate, whole grain rate, gel consistency, and taste score, while reducing the chalkiness rate, chalkiness degree, and amylose content. Moreover, the treatment with the addition of nano-magnesium was superior to that of ionic magnesium in terms of the improvement in brown rice rate, whole polished rice rate, and taste score. In terms of the physical and chemical properties of grain starch, the application of magnesium fertilizer significantly increased the highest viscosity and breakdown value of starch, while decreased the hot paste viscosity, cool gel viscosity, and setback value, further demonstrating the effectiveness of magnesium fertilizer in improving the cooking and taste quality of rice. In summary, applying an appropriate amount of magnesium fertilizer during the cultivation of Muyudao 49 can not only increase yield but also improve the quality of rice, with nano-magnesium fertilizer being more effective than ionic magnesium fertilizer.