The carbodiimide-driven reaction cycle has proven a powerful catalytic reaction in powering supramolecular machinery, self-assembly, and phase separation. Nevertheless, side reactions poison the catalyst, which is disastrous for these reaction cycles. We tested the effects of various parameters on suppressing side product Nacylurea in a carbodiimide-driven reaction cycle, including fuel structure, catalyst concentration, catalyst structure, additives, temperature, and pH. Increasing catalyst concentration results in less N-acylurea formation, but the influence wore off. Precursors with two carboxylic groups tend to form intramolecular anhydrides with less Nacylurea. However, N-acylurea formation becomes more favored if the two carboxylic groups are far apart. Moreover, pyridine performed best, but its ability also wore off with increasing concentration. Low temperature and low pH gave a higher effective reaction cycle. Hence, a combination of low temperature, low pH, and 10% pyridine as a fuel fraction is the optimal condition for a highly effective carbodiimide-driven cycle. We believe our work would provide helpful suggestions for using carbodiimide-fueled reaction cycles to regulate molecular function about how to choose an optimal condition.