Lithium-ion rechargeable batteries have attracted considerable research enthusiasm and meanwhile achieved great successes in industry during the past three decades. To meet the ever-increasing demand of batteries safety especially for the application in electric vehicles and energy storage devices, phosphorus-based flame retardants as additives have been developed and investigated. Herein, trivalent and pentavalent phosphorus-based flame retardants are purposely employed to comparably investigate the influence on safety and electrochemical performance of Li-ion batteries. The results show that pentavalent phosphorus-based electrolytes possess wider electrochemical windows and can endure higher voltage compared to trivalent phosphorus-based electrolytes, revealing that pentavalent phosphorus-based flame retardants are more suitable as efficient additives for cathode materials systems. Interestingly, trivalent phosphorus flame retardants may act as solid electrolyte interphase layer formers, which can be decomposed and meanwhile promote the formation of stable solid electrolyte interphase layer on the surface of graphitic anode materials even with a low loading. Moreover, it is worth noting that both trivalent and pentavalent phosphorus flame retardants show potential for application in high rate performance. This work can provide help for scientific research or industry in the study of phosphorus-containing flame retardants for batteries.