Abstract: Natural products areone source of new drugs, and their target identification is pivotal forelucidating the mechanism of action. Most methods of target discovery and validation utilize labeling natural products with probes. This is time-consuming and laborious, and often results in activity decrease or change of the natural products. Recent methods withoutchemicalmodificationhave become the main force in the target identification of natural products, including direct or indirect methods. Direct methods are mainly based on the principle of affinity and stability of protein, and indirect methods infer the drug target from the change in physiological responses or biochemical signatures. This review summarizes recent methods for target identification and validation of label-freenatural products, providing new ideas and strategies for future research in natural products.