For the past decades, the low-temperature phase of Ca3Ru2O7 below the 48K first-order phase transition remains a puzzle with controversial suggestions involving metallic ferroelectric, orbital or magnetic ordering. Through analysis of experimental lattice structure, density functional theory calculation, and effective model analysis, we propose that the 48K phase transition is a bond formation transition promoted by the magnetism mediated orbital re-polarization. Most interestingly, this transition is accompanied by a switch of two metallic ferroelectric orders from a xy + y symmetry to xz + z. Our study not only resolves a long-standing puzzle of this phase transition in this material, but also demonstrates perhaps the first example of transition between multiple emergent ferroelectric orders in bad metals, resulting from interplay between multiferroic orders.