One of the most important foundations for growth and development in individual and social life is learning. Today, mathematics disorder is considered as great obstacles to academic achievement and learning of individuals. The main objective of this study was to investigate the effectiveness of cognitive therapy based on "sympathetic mind" on modifying maladaptive schemas and reducing negative emotions in students with mathematics disorder. This research was an experimental study including pre-test and post-test with a control group. The statistical population of the study included middle school students in Delfan city in the academic year 2013-14, who were identified as having mathematical learning disabilities. The sample size consisted of 40 female students with mathematics learning disabilities. After students were identified by the Key Math Scale (KMS) and a structured clinical interview they were randomly assigned to an experimental and a control group. The Short Early Maladaptive Schema Questionnaire and the Young Positive and Negative Emotions Questionnaire were used. For both groups the Pre-test and post-test was performed. The intervention group received compassionate-mind training for 12 sessions of 90 minutes while the control group received no intervention. Results of multivariate analysis of covariance (MANCOVA) showed that intervention significantly reduced maladaptive schemas and negative emotions of female students with mathematics disorder. This finding has important implications as regards the education and mental health of students. It is suggested that this treatment program be used in schools and clinics as a complimentary method to other treatments in order to reduce negative emotions and prevent the formation of maladaptive schemas in   high school students.