The goal of document-level relation extraction (DocRE) is to identify relations between entities from multiple sentences. As a multi-label classification task, a common approach is to determine whether there are relations for an entity pair by selecting a multi-label classification threshold, with scores of relations above the threshold predicted as positive and the rest as negative. However, we find that predicting multiple relations for entity pairs causes the decrease of predicted scores in positive classes. This could lead to many positive classes being incorrectly predicted as negative. Additionally, our analysis suggests that fitting the distribution of predicted relations to the prior distribution of relations can help improve prediction performance. However, previous studies have not explored or leveraged the prior distribution of relations. To address these issues and findings, we for the first time propose the idea of incorporating the relational prior distribution into the loss calculation in DocRE tasks. We innovatively propose an Adaptive Relational Prior Distribution Loss (ARPDL), which can adaptively adjust relation prediction scores based on the relational prior distribution. Our designed relational prior distribution component can also be integrated as an adapter into other threshold-based losses to improve prediction performance. Experimental results demonstrate that ARPDL consistently improves the performance of existing DocRE models, achieving new state-of-the-art results. Furthermore, integrating our relational prior distribution adapter into other losses significantly enhances their performance in DocRE tasks, validating the effectiveness and generality of our approach. Code is available at https://github.com/xhm-code/ARPDL.