Regional rainfall-runoff modeling is a classic and significant research topic in hydrological sciences. Currently, the predominant modeling approach is developing data-driven models. This study proposes a rainfall-runoff model named ED-TimesNet (Encoder–Decoder-based TimesNet), which consists of convolutional neural networks. It transforms a one-dimensional time series into a two-dimensional matrix based on frequency-domain partitioning rules and subsequently employs a two-dimensional visual backbone to learn both local and global features of the hydrological time series. Compared to LSTM-based models and Transformer models, this model learns both intra-period and inter-period variations in hydrological series, simultaneously focusing on the relationships between adjacent and non-adjacent time points. It alleviates the temporal ambiguity problem inherent in attention mechanisms. This research validates the performance of the ED-TimesNet model in regional rainfall-runoff modeling tasks using the Catchment Attributes and Meteorology for Large-sample Studies (CAMELS) dataset. The model achieves a median and mean NSE of 0.8049 and 0.7808, respectively, across 448 basins, outperforming the benchmark LSTM, VIC, and mHM models, and achieving comparable performance to the Transformer model. This paper does not address the model’s performance on ungauged basins. The method of predicting runoff based on the periodic features of hydrological data provides a novel perspective for hydrological sciences.