Field phenotyping is a crucial process in crop breeding, and traditional manual phenotyping is labor-intensive and time-consuming. Therefore, many automatic high-throughput phenotyping platforms (HTPPs) have been studied. However, existing automatic phenotyping methods encounter occlusion problems in fields. This paper presents a new in-field interactive cognition phenotyping paradigm. An active interactive cognition method is proposed to remove occlusion and overlap for better detectable quasi-structured environment construction with a field phenotyping robot. First, a humanoid robot equipped with image acquiring sensory devices is designed to contain an intuitive remote control for field phenotyping manipulations. Second, a bio-inspired solution is introduced to allow the phenotyping robot to mimic the manual phenotyping operations. In this way, automatic high-throughput phenotyping of the full growth period is realized and a large volume of tiller counting data is availed. Third, an attentional residual network (AtResNet) is proposed for rice tiller number recognition. The in-field experiment shows that the proposed method achieves approximately 95% recognition accuracy with the interactive cognition phenotyping platform. This paper opens new possibilities to solve the common technical problems of occlusion and observation pose in field phenotyping.