The present invention provides a lithium ion secondary battery having superior storage characteristics at high temperatures and superior high voltage characteristics and a nonaqueous electrolyte used therein. The present invention is a lithium ion secondary battery provided with a positive electrode, negative electrode, and nonaqueous electrolyte that includes a nonaqueous solvent and electrolyte salt. The lithium ion secondary battery is characterized by the nonaqueous solvent containing a fluorine-containing ether shown by general formula (1): Rf1-O-Rf2 (1) (in the formula, Rf1 and Rf2 are the same or different and are a C1-10 alkyl group or C1-10 fluoroalkyl group; where either or both of Rf1 and Rf2 is a fluoroalkyl group) and containing the compounds shown in (I) and (II) at a total of 5000 ppm or less to the fluorine containing ether. (I) Fluorine-containing unsaturated compound (II) General formula (2): Hydroxyl group-containing compound shown by Rf1OH (2) (In the formula, Rf1 is the same as described previously).