Since the discovery of the first peroxidase nanozyme (Fe3O4), numerous nanomaterials have been reported to exhibit intrinsic enzyme‐like activity toward inorganic oxygen species, such as H2O2, oxygen, and O2•‐. However, the exploration of nanozymes targeting organic compounds holds transformative potential in the realm of industrial synthesis. This review provides a comprehensive overview of the diverse types of nanozymes that catalyze reactions involving organic substrates and discusses their catalytic mechanisms, structure‐activity relationships, and methodological paradigms for discovering new nanozymes. Additionally, we propose a forward‐looking perspective on designing nanozyme formulations to mimic subcellular organelles, such as chloroplasts, termed “nano‐organelles”. Finally, we analyze the challenges encountered in nanozyme synthesis, characterization, nano‐organelle construction and applications while suggesting directions to overcome these obstacles and enhance nanozyme research in the future. Through this review, our goal is to inspire further research efforts and catalyze advancements in the field of nanozymes, fostering new insights and opportunities in chemical synthesis.