In contemporary philosophy of mind, naturalist theory is dominant in areas where there are attempts to explain what a human being is. Naturalism is roughly the idea that reality contains no supernatural element. In the field of the mind-body problem, this idea often stands out in a reductionist manner. When the mind is wanted to be reduced to the body, sometimes the naturalistic explanation of mental phenomena such as qualia, intentionality, free will, and language does not seem sufficient. Therefore, there are cases where the explanatory power of naturalism on mental phenomena is weak. This article aims to explain Chomsky's critique of naturalism and at the same time the construction of his own naturalism, who realizes that the explanatory power of naturalism is weak. In this direction firstly, naturalism and its problems are tried to be explained. Then, the ground of Chomsky's criticism of naturalism is mentioned. Methodological naturalism, which is Chomsky's alternative naturalism, which is the naturalist understanding produced by the ground in question, is included. Chomsky provided supporting data to methodological naturalism through the philosophy of science. In this context, Chomsky's criticisms of situations where the ideal of inter-scientific unity turns into an ideology of scientism are mentioned. Chomsky, with examples from the history of science, mentions that some phenomena that are outside the scope of science may enter the limits of science over time. While defending the obedience to the rules and method set by science, he also develops a theory of naturalism by criticizing the limits of science. Chomsky explains methodological naturalism through his views on linguistics. For this reason, the meaning of Chomskyan linguistic views in methodological naturalism are clarified in this study. As a result, it is possible to say that Chomskyan understanding of science and language theory both approve and criticize naturalism, producing a moderate, form of naturalism.