With the expansion of muskmelon cultivation, manual pollination is increasingly inadequate for sustaining industry development. Therefore, the development of automatic pollination robots holds significant importance in improving pollination efficiency and reducing labor dependency. Accurate flower detection and localization is a key technology for enabling automated pollination robots. In this study, the YOLO-MDL model was developed as an enhancement of YOLOv7 to achieve real-time detection and localization of muskmelon flowers. This approach adds a Coordinate Attention (CA) module to focus on relevant channel information and a Contextual Transformer (CoT) module to leverage contextual relationships among input tokens, enhancing the model’s visual representation. The pollination robot converts the 2D coordinates into 3D coordinates using a depth camera and conducts experiments on real-time detection and localization of muskmelon flowers in a greenhouse. The YOLO-MDL model was deployed in ROS to control a robotic arm for automatic pollination, verifying the accuracy of flower detection and measurement localization errors. The results indicate that the YOLO-MDL model enhances AP and F1 scores by 3.3% and 1.8%, respectively, compared to the original model. It achieves AP and F1 scores of 91.2% and 85.1%, demonstrating a clear advantage in accuracy over other models. In the localization experiments, smaller errors were revealed in all three directions. The RMSE values were 0.36 mm for the X-axis, 1.26 mm for the Y-axis, and 3.87 mm for the Z-axis. The YOLO-MDL model proposed in this study demonstrates strong performance in detecting and localizing muskmelon flowers. Based on this model, the robot can execute more precise automatic pollination and provide technical support for the future deployment of automatic pollination robots in muskmelon cultivation.