Given an elliptic curve $E$ defined over $\mathbb{C}$, let $E^{\times}$ be an open subset of $E$ obtained by removing a point. In this paper, we show that the $i$-th Betti number of the unordered configuration space $\mathrm{Conf}^{n}(E^{\times})$ of $n$ points on $E^{\times}$ appears as a coefficient of an explicit rational function in two variables. We also compute its Hodge numbers as coefficients of another explicit rational function in four variables. Our result is interesting because these rational functions resemble the generating function of the $\mathbb{F}_{q}$-point counts of $\mathrm{Conf}^{n}(E^{\times})$, which can be obtained from the zeta function of $E$ over a finite field $\mathbb{F}_{q}$. We show that the mixed Hodge structure of the $i$-th singular cohomology group $H^{i}(\mathrm{Conf}^{n}(E^{\times}))$ with complex coefficients is pure of weight $w(i)$, an explicit integer we provide in this paper. This purity statement implies our main result about the Betti numbers and the Hodge numbers. Our proof uses Totaro's spectral sequence computation that describes the weight filtration of the mixed Hodge structure on $H^{i}(\mathrm{Conf}^{n}(E^{\times}))$.