The estimation of direction of arrival (DOA) is a crucial issue in conventional radar, wireless communication, and integrated sensing and communication (ISAC) systems. However, low-cost systems often suffer from imperfect factors, such as antenna position perturbations, mutual coupling effect, inconsistent gains/phases, and non-linear amplifier effect, which can significantly degrade the performance of DOA estimation. This paper proposes a DOA estimation method named super-resolution DOA network (SDOA-Net) based on deep learning (DL) to characterize the realistic array more accurately. Unlike existing DL-based DOA methods, SDOA-Net uses sampled received signals instead of covariance matrices as input to extract data features. Furthermore, SDOA-Net produces a vector that is independent of the DOA of the targets but can be used to estimate their spatial spectrum. Consequently, the same training network can be applied to any number of targets, reducing the complexity of implementation. The proposed SDOA-Net with a low-dimension network structure also converges faster than existing DL-based methods. The simulation results demonstrate that SDOA-Net outperforms existing DOA estimation methods for imperfect arrays.