A new ratoon rice cropping method known as the SALIBU system, which uses the lower nodes of the stubble, is gradually spreading throughout the tropical regions. In a previous study, the technology package, ‘cutting twice’ has a large effect on the number of ratoons (tillers), and interestingly, the effect has a large positive effect under poor management conditions, but a medium negative effect under standard management conditions. The conditions included fertilizing, water management, and growth stage at harvesting; however, which of these conditions has the greatest effect on the effect of ‘cutting twice’ remains unclear. We performed a pot experiment focusing on fertilizer and timing of harvesting, to clarify which of the level of fertilizer or the delay of harvesting time affects the number of ratoons. The results showed that with a short delay in harvesting there were almost no ratoons, a long delay in harvesting resulted in many ratoons. This indicates the negative effect of cutting twice occur due to earlier harvesting. Generally, the growth of ratoons depends on the carbohydrate reserves of the stubble. Hence, in the case of a single harvest, the ratoons decrease with the delay in harvesting. On the other hand, cutting the stem increases dead buds in the nodes closer to the ground. Namely, the second cut will remove the high node buds and reduce the incidence of ratoons. As for adding fertilizer results in more ratoons steadily. Harvesting earlier (at the physiological maturation stage; 25% green husk) than normal is emphasized in the SALIBU technology package. However, our results show the ‘cutting twice’ reduces the number of ratoons when harvesting early.