6-amino-1,3-dimethyl-5-nitrosouracil (NAU) is an important intermediate for the synthesis of caffeine and theophylline, usually in the form of monohydrate. However, NAU·H₂O is aggregated and has a plate-like habit, which is very unfavorable for downstream process such as filtration and transportation. In this work, carboxymethylcellulose (CMC), a very common polymer, was selected as an additive to manipulate the habit of NAU·H₂O. It was found that under acidic conditions, the addition of CMC can change the habit from plate-like to block-like and can significantly improve the aggregation. On the contrary, the additive cannot change the habit under neutral or weakly alkaline conditions. The underlying mechanism was analyzed by experiment and molecular dynamics simulation. It is found that, under neutral or alkaline conditions, CMC will dissociate into negatively charged polymer chains, which have a stronger interaction with water. But CMC will combine with hydrogen ions under acidic conditions, weakening the interaction with water, allowing it to adhere to the (0 0 1) face and inhibiting the growth of this face. The results of this study should be helpful in the selection and mechanism research of polymer additives for crystal habit.