Recently, deep learning-based fruit detection applications have been widely used in the modern fruit industry; however, the training data labeling process remains a time-consuming and labor-intensive process. Auto labeling can provide a convenient and efficient data source for constructing smart orchards based on deep-learning technology. In our previous study, based on a labeled source domain fruit dataset, we used a generative adversarial network and a fruit detection model to achieve auto labeling of unlabeled target domain fruit images. However, since the current method uses one species source domain fruit to label multiple species target domain fruits, there is a problem of the domain gap in both the foreground and the background between the training data (retaining the source domain fruit label information) and the application data (target domain fruit images) of the fruit detection model. Therefore, we propose a domain-adaptive anchor-free fruit detection model, DomAda-FruitDet, and apply it to the previously proposed fruit labeling method to further improve the accuracy. It consists of 2 design aspects: (a) With a foreground domain-adaptive structure based on double prediction layers, an anchor-free method with multiscale detection capability is constructed to generate adaptive bounding boxes that overcome the foreground domain gap; (b) with a background domain-adaptive strategy based on sample allocation, we enhance the ability of the model to extract foreground object features to overcome the background domain gap. As a result, the proposed method can label actual apple, tomato, pitaya, and mango datasets, with an average precision of 90.9%, 90.8%, 88.3%, and 94.0%, respectively. In conclusion, the proposed DomAda-FruitDet effectively addressed the problem of the domain gap and improved effective auto labeling for fruit detection tasks.