The input-output relation in control theory corresponds to the cause-effect relation among events. Based on causality between matters, this paper investigates the methodology problem in control theory, and proposes a cause-plant-effect(CPE) relationship based cause-effect control method.From the modeling perspective, the cause-plant-effect control method can be applied to describe the propagation of events, links between matters and rules, and can thus encompass a class of more generalized, more social and more intelligent control and optimization problems.From the analysis perspective, we propose the concepts of generalized controllability, generalized observability, generalized disturbance estimatability, compensatability and attenuatability for multi-cause-multi-effect systems to extend the domain of internality in traditional control theory. From the perspective of time sequence mechanism, the driving direction of causes and effects can be either forward or backward, presenting time inconsistency and non-causality/time inversion. The objective of control is to reduce the probability of unpredictable(adverse) effects and increase the probability of predictable(good) effects, under the influence of the uncontrollable(external) causes, via alternating the controllable(internal) causes.