To clarify the combined effects of the cutting time and cutting height on ratooning ability and rice grain yield of the ratoon crop in the novel ratoon rice cropping, a field experiment was carried out to investigate the combined effects of harvesting time and the stubble-cutting height of the main crop on the growth duration, ratooning ability and grain yield of the ratoon crop. The growth period was shortened by 3.5 days on average when the harvesting time was 10 days ahead of time. On average, the growth duration was prolonged by 7 days per each decrease of 10 cm stubble height. Early harvesting and increasing stubble-cutting height greatly increased the grain yield of the ratoon crop. The highest grain yield was achieved at 10 days after flowering stage and a stubble height of 30 cm, which were 6916 kg·hm−2 for XLY900 and 7262 kg·hm−2 for YY4149, averaged across years. High rice yield of the ratoon crop was mainly depended on panicle numbers and grain-filling percentage, rather than spikelets per panicle. Increasing cutting height and the cutting time of the main crop ahead maintain more stubble biomass and nitrogen content. A significant positive correlation was observed between stubble nitrogen content and tillers-to-stubble ratio (TSR), as well as a significant positive relation was found between panicle-to-stubble ratio and TSR. Therefore, cutting 10 days after flowering stage of the main crop with 30 cm stubble-cutting height enhances ratooning ability due to higher stubble biomass and nitrogen content, and then increases rice yield of the ratoon crop.