In supercapacitor energy storage system (SCESS), the DC bus voltage could be stabilized rapidly by controlling the bidirectional DC/DC converter. In order to suppress some bifurcation and chaos phenomena in the control process, a chaos control method for the SCESS application was proposed. The control principle of this method was analyzed. The discrete iteration model of bidirectional DC/DC converter was established by nonlinear dynamics theory. A chaos control signal which could automatically adjust the compensation slope was designed. The asynchronous switching function and synchronous switching mapping were solved numerically under the action of the chaos control signal, so that the bifurcation diagrams of the system could be drawn. Simulation and experiment showed that the bifurcation and chaos phenomena of SCESS could be effectively suppressed by the method. The stable working range and dynamic response speed of the system were improved.