The Complex System Theory comprehensively explores the role of complexes in individual psychological structures and their intricate dynamic interactions through three core concepts: complexes, complex trees, and complex chains. Based on Jung’s concept of complexes, this paper posits that complexes are not merely independent psychological units but form a complex network within the individual’ s psychological system in a hierarchical and dynamic manner. The complex tree reveals the hierarchical structure of complexes, helping individuals identify core complexes and their derivative secondary complexes. The complex chain, on the other hand, demonstrates the dynamic relationships and chain reactions of complexes, emphasizing their trigger mechanisms in emotions and behaviors. Through case analysis, this paper further illustrates the application of the complex system in psychological counseling and therapy, proving its practical effects in enhancing self-awareness, improving emotional regulation, and interpersonal relationships. The paper also suggests future directions for the development and research of complex system theory, including long-term case studies and its integration with other psychotherapeutic methods, to further verify the universality and clinical value of the theory.