A flag variety is a smooth projective homogeneous variety. In this paper, we study Newton-Okounkov polytopes of the flag variety $Fl(\mathbb{C}^4)$ arising from its cluster structure. More precisely, we present defining inequalities of such Newton-Okounkov polytopes of $Fl(\mathbb{C}^4)$. Moreover, we classify these polytopes, establishing their equivalence under unimodular transformations.