Ethephon (2-chloroethyl phosphonic acid) is a plant growth promoter used to control the plant growth process by liberating ethylene and stimulating the production of endogenous ethylene. Medicinal plants are sources of novel drug discovery targets. Costus (Saussurea lappa) has been used as traditional Chinese medicine. The current study was conducted to examine the possible modifying effects of costus (S. lappa) root aqueous extract against kidney toxicity induced by ethephon in male rats. A total of 50 adult male rats were divided into five groups (first, control; second, costus; third, ethephon; fourth, posttreated ethephon with costus; fifth, ethephon self-healing). There is a significant increase in the serum levels of urea, creatinine, potassium ions, chloride ions, kidney injury, DNA damage, and proliferating cell nuclear antigen expressions in treated rats with ethephon when compared to the control group. In contrast, the treated rats with ethephon revealed a significant decrease in the levels of sodium ions and an insignificant decrease in the calcium ions. Saussurea lappa extract modified these alterations when compared to the control group. As a result, costus root extract significantly reduced rat kidney toxicity after ethephon administration. We recommend costus to be included in diet for its valuable effects, and also producers and consumers should become more aware about the toxic effects of ethephon.