With the rapid development of computer vision, the application of computer vision to precision farming in animal husbandry is currently a hot research topic. Due to the scale of goose breeding continuing to expand, there are higher requirements for the efficiency of goose farming. To achieve precision animal husbandry and to avoid human influence on breeding, real-time automated monitoring methods have been used in this area. To be specific, on the basis of instance segmentation, the activities of individual geese are accurately detected, counted, and analyzed, which is effective for achieving traceability of the condition of the flock and reducing breeding costs. We trained QueryPNet, an advanced model, which could effectively perform segmentation and extraction of geese flock. Meanwhile, we proposed a novel neck module that improved the feature pyramid structure, making feature fusion more effective for both target detection and instance individual segmentation. At the same time, the number of model parameters was reduced by a rational design. This solution was tested on 639 datasets collected and labeled on specially created free-range goose farms. With the occlusion of vegetation and litters, the accuracies of the target detection and instance segmentation reached 0.963 ([email protected]) and 0.963 ([email protected]), respectively.