Melatonin mediates many physiological processes in plants. We investigated its role in regulating growth, potassium uptake, and root system architecture under three types of stress: salinity or a deficiency of all nutrients in Malus hupehensis Rehd., as well as a K deficiency in Malus rockii Rehd. Each treatment caused a reduction in growth rates and disrupted the absorption of potassium. However, pretreatment with 0.1 mmol/L melatonin significantly alleviated such inhibitions. The addition of melatonin also upregulated genes for antioxidant enzymes involved in the ascorbate-glutathione cycle (MdcAPX, MdDHAR1, MdDHAR2, MdMDHAR, and MdcGR) and helped decrease the accumulation of H2 O2 while improving the expression of K transporters and genes for the CBL1-CIPK23 pathway. These results indicated that melatonin can regulate the ROS signal and activate the CBL1-CIPK23 pathway to regulate the expression of a potassium channel protein gene, thereby promoting the absorption of potassium ions. Our findings demonstrate that inducing melatonin production is an important mechanism for plant defenses that can serve as a platform for possible applications in agricultural or related fields of research.