Objectives: The aim of the present study was comparison between the efficacy of Transdiagnostic Therapy Based on Repetitive Negative Thoughts (TTRNT) with Unified Transdiagnostic (UT) therapy in treatment of patients with co-occurrence anxiety and depressive disorders. Method: In the present study, 45 patients with at least one principle diagnosis and one co-principle in the field of anxiety and depressive disorders randomly assigned to three groups of TTRNT, UT as well as waiting list group. Two treatment groups received correspondent treatments. For data collection, the participants completed the Beck Depression Inventory-second edition (BDI-II), Beck Anxiety Inventory (BAI), Positive and Negative Affect Scale (PANAS) and the Work and Social Adjustment Scale (WSAS) during the three stages of pre-test, post-test and a period of six-month follow-up. The data of the study were analyzed through analysis variance with mixed repeated measures, post-hoc main effect, and clinical significance changes criteria. Results: The results of the present study demonstrated that both treatments in comparison with waiting list decreased the symptoms of the patients with co-occurrence anxiety and depressive disorders (p<0.001). However, the TTRNT was more effective than UT in improvement of anxiety, general function, and negative affect (p<0.05), but there was not any meaningful difference between these two treatments in decreased the depression (p>0.05). Also, the UT has better function in increasing the positive affect (p<0.05). Furthermore, evaluation of the clinical significance changes criteria indicated that the group of TTRNT for principle and co-principle diagnosis achieved to 23% and 29% more than UT group in high end-state functioning (HESF) at the end of follow-up period, respectively. Conclusion: The transdiagnostic therapy based on repetitive negative thoughts is more effective than unified transdiagnostic therapy in improving the symptoms of the patients with the co-occurrence anxiety and depressive disorders.