Birds flying collectively is a fascinating phenomenon in nature, which is central in ethological studies. Owing to the difficulty of introducing controlled variables into a natural bird flock, current animal behavior paradigms limit our understanding of collective behavior and mechanism. The recently developed technology of robo-pigeon, which allows behavior regulation over organisms through brain microstimulation, can potentially serve to design the controlled variables. However, it still poses challenges for unrestrained animals outdoors. Here we report the first application of robo-pigeon to the study of collective behavior, illustrating how intact pigeons in a flock interact with a program-controlled robo-pigeon. The controlled variable of direction manipulation introduced by the robo-pigeon may balance their preferred directional choice in the flock. Its effectivity depends on the hierarchical level to which the robo-pigeon belongs. This study suggests that direct manipulation of flight trajectories by a robo-pigeon might be a useful causal tool to study the collective behavior of bird flocks.