The invention belongs to the field of environmental governance and discloses a strain of burkholderia cenocepacia tolerant to heavy metals and an effect of the burkholderia cenocepacia in removing heavy metals, wherein the strain is stem endophyte Burkholderia sp.WJ-19 separated from the sapium discolor planted in a heavy metal mining area. The burkholderia cenocepacia WJ-19 is highly tolerant tosouthern typical heavy metals lead, zinc and cadmium, and has high efficiency in removing zinc and cadmium in an aqueous solution, and can grow in a culture solution with high concentration of heavy metals zinc and cadmium without experiencing obvious inhibition. The WJ-19 provides a new material for microbial control of heavy metal pollution, and has potential in development and application.