In a lithium ion secondary battery including a positive electrode, a negative electrode containing an alloy-based negative electrode active material, a separator, a positive electrode lead, a negative electrode lead, a gasket, and an outer case, the positive electrode is allowed to contain an oxygen deficient non-stoichiometric oxide, or an oxygen removing layer containing an oxygen deficient non-stoichiometric oxide is provided between the positive electrode and the separator. In a lithium ion secondary battery containing the alloy-based negative electrode active material, a reaction between oxygen generated in the positive electrode and the alloy-based negative electrode active material, and heat generation accompanying the reaction are prevented.