Introduction: The present study is conducted with the aim of studying the efficacy of metacognition training and perception of spatial relationship on improvement of mathematical operation of the students with mathematics learning disabilities.Method: The statistical population of the study included the students of grade three, primary school, with mathematics learning deficiencies in Isfahan between the years1389-90. To do this study 20 classes were sampled randomly. The applied instruments included Wechsler Intellectual Scale for Children 4, the test of recognizing mathematics deficiencies and the test of mathematics function. From among the students who were recognized with mathematics deficiencies, 45 were selected randomly for metacognition training, perception of spatial relationship training, and control groups.Experimental research design was in pre-test/post-test with a control group. Data were analyzed by statistical covariance.Results: The covariance analysis represented a significant difference between the two groups: (F2, 41=18/12, h=0/47, P<0/0001) the test revealed the least significant difference between metacognitive training group (p<0.0001) and perception of spatial relationship group (p<0.0001) and control group, while there was no significant difference between the experimental groups (P=0.991).Conclusion: Based on the findings of this study, both metacognitive methods and perception of spatial relationship methods of training are useful in treatment of mathematics learning disorders.Findings of the present study may conclude that it is useful to apply metacognition and perception of spatial relationship in teaching mathematics to the students.