Vermicompost is an excellent organic fertilizer, but the application of vermicompost in fragrant rice production has not yet been reported. Seedling nursery is an important component of rice production. The present study firstly applied vermicompost in fragrant rice production through nursery raising. The seedlings of three fragrant rice cultivars were raised in matrix with different rations of vermicompost (the treatment without vermicompost was taken as the control), and the growth parameters and physiological characters of seedlings were investigated. The results showed that, compared with the control, the application of vermicompost significantly (p < 0.05) increased the plant height, stem diameter, fresh weight, and dry weight of fragrant rice seedlings by 11.22–24.73%, 38.34–65.87%, 16.74–30.46%, and 16.61–35.16%, respectively. Nursery raising with vermicompost significantly (p < 0.05) enhanced the net photosynthetic rate by 5.99–12.93%, relative to the control. Higher contents of chlorophyll a, chlorophyll b, carotenoids, and total chlorophyll were recorded in vermicompost treatments than in the control. Compared with the control, vermicompost treatments also increased root length, surface area, mean diameter, root volume, root tip number, and root activity of fragrant rice seedlings by 12.42–27.82%, 15.04–38.65%, 12.64–23.12%, 42.41–63.58%, 18.62–24.95%, and 12.01–26.29%, respectively. Moreover, nursery raising with vermicompost enhanced the activities of antioxidant enzymes including superoxide, peroxidase, and catalase by 7.97–24.21%, 17.11–44.99%, and 7.37–15.95%, respectively, relative to the control. Moreover, 7.92–29.40% lower malondialdehyde contents were recorded in vermicompost treatments compared with the control. Therefore, nursery raising with vermicompost could be a good agronomy practice in machine-transplanted fragrant rice.