In this paper, we concern with the classification of complex prime $\mathbb{Q}$-Fano $3$-folds of anti-canonical codimension 4 which are produced, as weighted complete intersections of appropriate weighted projectivizations of certain affine varieties related with $\mathbb{P}^{1}\times\mathbb{P}^{1}\times\mathbb{P}^{1}$-fibrations. Such affine varieties or their appropriate weighted projectivizations are called key varieties for prime $\mathbb{Q}$-Fano 3-folds. We realize that the equations of the key varieties can be described conceptually by Freudenthal triple systems (FTS, for short). The paper consists of two parts. In Part 1, we revisit the general theory of FTS; the main purpose of Part 1 is to derive the conditions of so called strictly regular elements in FTS so as to fit with our description of key varieties. Then, in Part 2, we define several key varieties for prime $\mathbb{Q}$-Fano 3-folds from the conditions of strictly regular elements in FTS. Among other things obtained in Part 2, we show that there exists a $14$-dimensional factorial affine variety $\mathfrak{U}_{\mathbb{A}}^{14}$ of codimension $4$ in an affine $18$-space with only Gorenstein terminal singularities, and we construct examples of prime $\mathbb{Q}$-Fano $3$-folds of No.20544 in [GRDB] as weighted complete intersections of the weighted projectivization of $\mathfrak{U}_{\mathbb{A}}^{14}$ in the weighted projective space $\mathbb{P}(1^{15},2^{2},3)$. We also clarify in Part 2 a relation between $\mathfrak{U}_{\mathbb{A}}^{14}$ and the $G_{2}^{(4)}$-cluster variety, which is a key variety for prime $\mathbb{Q}$-Fano 3-folds constructed in [CD].