Ulva compressa, known as the green tide forming species, was reported that can adapt to hypo-salinity conditions such as estuaries and brackish lakes. To understand the underlying molecular mechanisms of hypo-salinity stress tolerance, a genome-wide gene expression profiles in U. compressa was performed using digital gene expression profile (DGE). This dataset includs 4 different time points(1h, 6h, 24h, 72h) in hypo-salinity stress and recovery. Our work will serve as an essential foundation for the understanding of the tolerance mechanism of U. compressa under the fluctuating salinity conditions.