A field study to optimize the nitrogen (N) top-dressing mode of panicle fertilization and improve rice yields was conducted in mid-eastern China. Japonica cultivar Yunongjing-6 was grown and panicle N fertilizer was applied at the beginning of the inverted fourth leaf stage using three different modes: manual broadcast application (BA) on the soil surface as a control treatment, deep application during ditching at a depth of 15 cm (DD) and manual BA on the soil surface during deep ditching (BAD). The activity of soil enzymes, including invertase, urease, phosphatase and catalase, was increased significantly at the jointing, booting and grain-filling stages with the DD and BAD treatments compared with the traditional BA mode. The DD and BAD treatments also increased basal internode and neck-panicle internode bleeding intensity. The DD treatment gave the highest crop yield, increasing the yield by 0.63 and 0.31 t/hm2 in 2011 and 2012, respectively, compared with BA. The results suggest that ditching during panicle N fertilizer application after sun-drying of the fields increases rice yields, most likely by improving the activity of soil enzymes and enhancing the physiological activity of roots and grain weight.