To enable fast charging of lithium ion batteries, extensive attention is needed to reduce the heat generation rate to avoid thermal runaway. This work studies the impact of the fast charging protocol on thermal behavior and energy efficiency of a lithium ion battery cell for 30-minute charging with 80% rated capacity. A two-stage constant current (2SCC) charging protocol with different current level combinations is adopted to mitigate the temperature rise leading to thermal runaway and improve the charging energy efficiency, because different charging current will generate different rates of heat. An electrochemical thermal coupled model is developed to predict the heat generation rate, charging energy rate, and temperature rise with experimental validation. The simulation results indicate that the “high-low” charging protocols of the 2SCC fast charge can achieve a lower overall temperature rise and higher charging energy efficiency than both the “low-high” charging protocols and the standard one-stage constant current (1SCC) charging. Compared to the 1SCC charge, the 2SCC charging protocol can improve the overall charging energy efficiency by 1%. Additionally, the impact of the 2SCC charging protocol on the thermal behavior under different initial cell temperatures and the heat transfer coefficients are discussed.