Cherry is an important fruit tree with delicious taste and high economic value, which have been planted worldwide. However, this species cannot withstand the presence of excessive amount of water; submergence injury sometimes occurs during cultivation of cherry and results in severe economic losses. By using a submergence-tolerant germplasm Prunus serrulata "Yimeng" and a submergence-sensitive germplasm Prunus pseudocerasus "Aihua" as test materials, this study cloned PsERF and PsCIPK, which are related to submergence tolerance in cherry, and analyzed the expression of PsERF and PsCIPK in submergence-tolerant and submergence-sensitive germplasms under submergence stress; moreover, the consistency and correlation of such expression with carbohydrate metabolism and plant growth-related genes (PsPDC, PsSUS, PsRAMY, and PsEXP) were analyzed. The results showed that PsERF and PsCIPK influence the expression of PsPDC, PsSUS, PsRAMY, and PsEXP at different extents under submergence and during recovery to systematically improve the submergence resistance of P. serrulata "Yimeng". This study lays the important theoretical and practical foundation for molecular improvement and germplasm innovation in submergence tolerance in cherry through genetic engineering.