A method and an apparatus for controlling a distributed automation system, wherein the method comprises determining global constraint rules according to the cooperative relationships between function blocks in the distributed automation system, and establishing a mathematical model based on Membrane Calculus, performing the instantiation of the established mathematical model based on Membrane Calculus according to an executor corresponding to each of the function blocks in the distributed automation system, so as to produce control logics for output to the distributed automation system. If disturbance information is received from the distributed automation system, altering the parameters of the instantiation of the mathematical model based on Membrane Calculus are altered using the disturbance information, so as to produce control logics for outputting to said distributed automation system. The present invention is capable of effectively dealing with all types of unpredictable disturbances, thus improving the adaptability thereof.