Potassium (K) deficiency is one of the major abiotic stresses which has drastically influenced maize growth and yield around the world. However, the physiological mechanism of K deficiency tolerance is not yet fully understood. To identify the differences of root morphology, physiology and endogenous hormones at different growing stages, two maize inbred lines 90-21-3 (tolerance to K deficiency) and D937 (sensitive to K deficiency) were cultivated in the long-term K fertilizer experimental pool under high potassium (+K) and low potassium (-K) treatments. The results indicated that the root length, volume and surface area of 90-21-3 were significantly higher than those of D937 under -K treatment at different growing stages. It was noteworthy that the lateral roots of 90-21-3 were dramatically higher than those of D937 at tasselling and flowering stage under-K treatment. Meanwhile, the values of superoxide dismutase (SOD) and oxidizing force of 90-21-3 were apparently higher than those of D937, whereas malondialdehyde (MDA) content of D937 was obviously increased. Compared with +K treatment, the indole-3-acetic acid (IAA) content of 90-21-3 was largely increased under-K treatment, whereas it was sharply decreased in D937. On the contrary, abscisic acid (ABA) content of 90-21-3 was slightly increased, but that of D937 was significantly increased. The zeatin riboside (ZR) content of 90-21-3 was significantly decreased, while that of D937 was relatively increased. These results indicated that the endogenous hormones were stimulated in 90-21-3 to adjust lateral root development and to maintain the physiology function thereby alleviating K deficiency.