The interesting phenomenon of nonperiodical flow rate switching between a high level and a low level was found under certain flow conditions in a loop with a cross pipe. It is caused by generation and collapse of swirling flow through opposite laterals of the cross pipe. In this paper, control of this phenomenon is experimentally investigated by using air-flow test equipment at Re≒2×105. It is clear that the phenomenon depends on cross pipe structure, and a slight difference in structure brings the flow rate to a stable high level or a stable low level. As the turbulence intensity in the flow is high, the switching does not occur because swirling flow becomes difficult to form. The effects of the control flow injection for stabilizing such a phenomenon are also confirmed.