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The capacity fading of lithium iron phosphate batteries is related to its internal temperature and the growth of solid electrolyte (SEI). It is an effective way by controlling its internal temperature to mitigate capacity fading. This paper discusses the impact of pre-cooling and resting time on capacity fading and the growth of SEI. Results showed that the battery capacity increased and the thickness of SEI decreased if the pre-cooling was employed. Compared to 25 °C of ambient temperature, the thickness of SEI under 5 °C of pre-cooling temperature decreased by 404 nm, 386 nm, and 502 nm for 2C, 3C, and 5C discharge rate, respectively. The internal temperature of battery could be better cooled and therefore capacity increased with the increase of resting time. At 15 °C of pre-cooling temperature, the capacity increased by 3.8% if the resting time increased from 600 s to 2400 s. Therefore, the pre-cooling method could effectively mitigate capacity fading. The conclusion obtained in this paper could provide guidance for battery thermal management.