Every science that attempts to solve the unknown covers its path through a certain method. There are four major methods for acquiring knowledge, and each of them has its own limits and strengths. There may be some sciences that use a certain method while some others use other methods. These methods are as follows: rational method, transitional method, intuitive method, empirical method. The nature of subject of a science determines the method used by that science. Difference in methods can lead to the plurality of sciences. Any researcher makes use of certain method or methods for resolving his own problems. The philosopher Mulla Sadra is no exception. He would use his own method to solve the philosophical issues. The main question here is pertaining to the research method in his philosophy. Mulla Sadra claims that he uses rational method for resolving philosophical issues, and this is proved by his actions. However, we see the use of general intuition in the philosophical issues. Using other research methods in Mulla Sadra’s works is not along with rational method; rather, it is in line with helping the philosophical issues to grow. Mulla Sadra, in spite of using other methods, ends his issues finally with philosophical method, and this is a philosopher’s task.