In the realm of electric vehicles, optimizing the thermal management systems for lithium-ion batteries is crucial for enhancing performance and longevity. To improve the cooling effect of the indirect liquid cooling system, this study reports on the CFD investigation of two novel designs of variable cross-section overflow channels of manifold cold plates for lithium-ion batteries. However, the total volume of the overflow channel is kept the same as that of the traditional design. The first type (Type-1) is referred to as the flow-direction variable cross-section. The second type (Type-2) is referred to as the vertical flow-direction variable cross-section. The angle of the flow channels, which is defined using two non-dimension parameters of deflection coefficient (Type-1 (alpha, ɑ), Type-2 (beta, β)) varied ranging from 1/7, 1/5, 1/3, 1/2, 2, 3, 5, 7. The effect of the deflection coefficient on flow and heat transfer characteristics is reported in this study. The result from the new designs is benchmarked with that of the traditional overflow unit. After that, the CFD model is extended to include a manifold unit with 12 Type-2 overflow channel units. The water coolant ranging from 0.1 mL/s to 0.63 mL/s with a temperature of 293 K is set to flow in the flow channel with a uniform heat flux at the bottom boundary wall. The maximum temperature of the heating surface decreased from 305.65 K to 301.93 K, and the average temperature of the heating surface of Type 2 (β = 7, Qinlet = 0.105 mL/s) decreased by 3.65 K compared to the traditional overflow unit. The thermal resistance of the Type-2 overflow unit with β > 1 decreased by a maximum of 30 % in comparison to that of the traditional overflow unit under the same boundary condition. Although the pressure drop of the Type-2 overflow unit has increased, the maximum increase is no more than 19 % compared to the traditional overflow unit. Based on this, a manifold unit is designed containing 12 Type-2 overflow units (optimized design, β = 5). Comparative analysis was conducted under the uniform heat flux condition equivalent to a 5 C discharge of the battery within the range of inlet flow rates of 2–7.2 mL/s. The average temperature of the heating surface of the optimized design decreased by 3.65 K compared to the traditional manifold unit, when the inlet flow rate is 2.39 mL/s, and the mean absolute temperature deviation decreased by 48 %.