Let $(Z_n)$ be a supercritical branching process in an independent and identically distributed random environment $ξ$. We study the asymptotic of the harmonic moments $\mathbb{E}\left[Z_n^{-r} | Z_0=k \right]$ of order $r>0$ as $n \to \infty$. We exhibit a phase transition with the critical value $r_k>0$ determined by the equation $\mathbb E p_1^k = \mathbb E m_0^{-r_k},$ where $m_0=\sum_{k=0}^\infty k p_k$ with $p_k=\mathbb P(Z_1=k | ξ),$ assuming that $p_0=0.$ Contrary to the constant environment case (the Galton-Watson case), this critical value is different from that for the existence of the harmonic moments of $W=\lim_{n\to\infty} Z_n / \mathbb E (Z_n|ξ).$ The aforementioned phase transition is linked to that for the rate function of the lower large deviation for $Z_n$. As an application, we obtain a lower large deviation result for $Z_n$ under weaker conditions than in previous works and give a new expression of the rate function. We also improve an earlier result about the convergence rate in the central limit theorem for $W-W_n,$ and find an equivalence for the large deviation probabilities of the ratio $Z_{n+1} / Z_n$.