Nitrogen is a key component in the growth of crop plant. To increase the yield of crops, an enormous amount of nitrogen fertilizer is currently being used, which increases the total production cost and leads to environmental pollution by the residual nitrogen sources. For these reasons, researchers have tried to improve the crop’s nitrogen use efficiency (NUE) as a solution for reducing the amount of nitrogen fertilizer used. MicroRNAs are a class of small non-coding RNAs regulating the expression of target genes. Recent studies suggested that the expression pool of microRNAs changes in response to a variety of nutrient deficiencies and that such changes play important roles in adapting to or resisting the consequential nutritional stresses. Here, we aim to identify and characterize rice microRNAs whose expression changes upon nitrogen starvation and re-supplementation. By applying RNA-Seq, we observed that the expression of a set of genes involved in nitrogen assimilation was altered in response to nitrogen deprivation. We also found that a considerable number of microRNAs exhibited dynamic expression changes in a nitrogen supply state-dependent manner and that the expression of genes targeted by those differentially regulated microRNAs was altered reciprocally. Our study suggests that microRNAs may have roles in regulating the response of rice to nitrogen supply state and subsequently modulating NUE.