In a new family of V-based kagome metals RV$_6$Sn$_6$ (R = Sc, Y, La), only ScV$_6$Sn$_6$ was observed to exhibit the unusual charge density wave (CDW) with a $\sqrt{3}{\times}\sqrt{3}$ in-plane ordering and a tripling of the unit cell along the $c$-axis. However, the driving mechanism of such a $\sqrt{3}{\times}\sqrt{3}{\times}$3 CDW order is elusive. Here, using first-principles density-functional theory calculations, we demonstrate that the $\sqrt{3}{\times}\sqrt{3}{\times}$2 or $\sqrt{3}{\times}\sqrt{3}{\times}$3 CDW order is driven by a Jahn-Teller-like effect where the interlayer dimerization of Sn atoms in kagome bilayers is accompanied by a charge redistribution between such Sn atoms and its associated gap opening. It is revealed that the free energy of the $\sqrt{3}{\times}\sqrt{3}{\times}$3 phase becomes lower than that of the $\sqrt{3}{\times}\sqrt{3}{\times}$2 phase above $T_{\rm CDW}$ mostly due to the emergence of a large configurational entropy. Such a high-entropy phase shows dynamic fluctuations between its degenerate configurations but, as the temperature lowers below $T_{\rm CDW}$, it can be kinetically trapped to release a sizable entropy. Our findings not only identify the driving mechanism and order-disorder transition of the CDW in ScV$_6$Sn$_6$ but also provide an ideal platform for investigating strong CDW fluctuations in V-based kagome metals.