Let $\mu = (\mu_{1}, \mu_{2}, \ldots, \mu_{m})$ and $\nu = (\nu_{1}, \nu_{2}, \ldots, \nu_{n})$ be two partitions of a positive integer $d$. In this paper, the author considers degree $d$ branched coverings of $\mathbb{P}^{1}$ with at most two special points, $0$ and $\infty$. Specifically, the purpose of the author is to give a recursion formula for double Hurwitz numbers $H^{g}_{\mu, \nu}$ by the cut-join analysis. Here, $H^{g}_{\mu, \nu}$ denotes the number of genus $g$ branched covers of $\mathbb{P}^{1}$ with branching date corresponding to $\mu$ and $\nu$ over $0$ and $\infty$, respectively. Furthemore, as application, the author gets a polynomial identity for linear Goulden-Jackson-Vakil intersection numbers.