Background: Generally, the yield of ratoon rice is at most 50% of the main crop. However, a cropping method “SALIBU” achieved more yield than the main crop and could be used for the cultivation of perennial cropping. Although the SALIBU method is implementing 10 additional management practices to conventional method, the effect of each management practice is unclear. Therefore, we aimed to evaluate the effect size and the robustness of each management practice. Methodology: We evaluated the effect size using an L16 orthogonal array design pot experiment. For the robustness, we duplicated the experiment under both standard and checked whether the practice shows the same effect size. The bad conditions were low plant density, no fertilization, continuous flooding water management, and late harvesting. Results: The ratoon rice yield was proportional to the number of ratoon tillers used as in conventionally produced ratoon rice. Late cutting was most affected to the number of ratoon tillers. Importantly, this effect was reversed; the effect was positive under bad conditions, but was negative under standard conditions. Furthermore, late irrigation, a recommended management practice, had a robust negative effect on ratoon tillers and yield under both the conditions. Positive large effects were shown in the bad condition only. Discussion: Our results show that the SALIBU cropping method includes practices with unstable, negative, or minimal effects. The practices have unstable effects should be clarifying the interaction with the condition. The practices that have negative effects should exclude. Using practice on small effect size should depend on a cost-benefit analysis. Conclusions: SALIBU will be acceptable to the Mekong Delta triple cropping rice cultivation without the additional practice of original SALIBU cropping method. However, further work is needed to clarify the interaction between late cutting and the cultivation condition, and on the negative effect of late irrigation.