This paper deals with the multivariable control system of the distillation tower by applying multi-structures in MATLAB/Simulink for a binary mixture of benzene and toluene. Four structures configurations of the distillation are applied based on the level and temperature variables. The PID controller is used in all structures in multivariable. These structures are compared with different disturbances. The integral absolute error is a criterion to test the controller\\\’s performance under step change disturbances. The controller\\\’s performance was investigated by recording responses to disturbances in set-point of reflux ratio, flow-rate of top and bottom products. The step testing appears to be the single-ended temperature control with bottom and top-level structures to regulate the flow rate of the bottom and top products. The best structure is top-level, bottom level and condenser temperature because the column made more stable, the integral absolute error is minimum value and fast access to set-point value.