The invention discloses a berberine-chrysin pharmaceutical eutectic crystal and a preparation method thereof and belongs to the technical field of pharmaceutical crystallization. The berberine-chrysinpharmaceutical eutectic crystal is prepared by dissolving berberine hydrochloride, chrysin and sodium hydroxide in ethanol according the ratio; a eutectic crystal structure unit comprises berberine cations, chrysin anions and chrysin molecules at the mol ratio of 1 to 1 to 2 and a molecular formula is [C20H18N O4]+[C15H9O4]-2[C15 H10 O4]. The preparation method disclosed by the invention has theadvantages of simplicity and feasibility, low cost and high crystal yield; the relative bioavailability of the chrysin of the prepared pharmaceutical eutectic crystal in rats is remarkably improved relative to the relative bioavailability of the pure chrysin, and the relative bioavailability is 1.7 times as much as the relative bioavailability of the pure chrysin.