Nanomaterials (NMs) synthesized from natural sources have been attracting greater attention, due to their intrinsic advantages including biocompatibility, stimuli-responsive property, nontoxicity, cost-effectiveness, and non-immunogenic characteristics in the biological environment. Among various biomedical applications, a breakthrough has been achieved in the development of drug delivery systems (DDS). Biocompatibility is necessary for treating a disease safely without any adverse effects. Some components in DDS respond to the physiological environment, such as pH, temperature, and functional group at the target, which facilitates targeted drug release. NM-based DDS is being applied for treating cancer, arthritis, cardiovascular diseases, and dermal and ophthalmic diseases. Metal nanomaterials and carbon quantum dots are synthesized and stabilized using functional molecules extracted from natural sources. Polymers, mucilage and gums, exosomes, and molecules with biological activities are directly derived from natural sources. In DDS, these functional components have been used as drug carriers, imaging agents, targeting moieties, and super disintegrants. Plant extracts, biowaste, biomass, and microorganisms have been used as the natural source for obtaining these NMs. This review highlights the natural sources, synthesis, and application of metallic materials, polymeric materials, carbon dots, mucilage and gums, and exosomes in DDS. Aside from that, challenges and future perspectives on using natural resources for DDS are also discussed.