Organic synthesis chemistry plays a crucial role in supporting social sustainable development and finds widespread applications across various fields. Electrocatalysis, with its benefits of high efficiency, mild reaction conditions, controllability, and environmental friendliness, stands out as one of the most effective strategies for driving the transformation of organic substrates. In recent years, nanocrystals (NCs) and single atom catalysts (SACs) have garnered significant attention in the realm of electrocatalytic organic transformation. This article presents a comprehensive overview of the applications of NCs and SACs in electrocatalytic organic transformation. It delves into advanced catalysts for electrocatalysis of representative substrates, covering both anodic oxidation and cathodic reduction aspects, and addresses their synthesis, characterization, catalytic mechanism, and performance. The ultimate goal of this review is to serve as a valuable reference and a source of inspiration for further exploration into the development of more effective catalysts for electrocatalytic organic transformation.