There are many different approaches to psychotherapy. Research indicates comparable effectiveness of various therapies, despite having different theoretical assumptions and using different therapeutic methods. In recent years, many researchers have attempted to understand such results by investigating specific and common factors in psychotherapy. It has been suggested that further developments in the field should aim to investigate factors underlying mental health problems and the principles informing the process of change in psychotherapy. In the current article, we will present perceptual control theory as a scientifically grounded approach that integrates theory and practice. Transdiagnostic principles explain the sources of emotional distress and the process of psychological change in psychotherapy. The main aim of the article is to introduce method of levels therapy, which has been created as a direct application of perceptual control theory principles. Description of the process of therapy is accompanied by clinical examples.