Soft rot disease caused by Botryosphaeria dothidea is one of the most important fungal diseases affecting kiwifruit production. The symptoms of the disease generally appear during the fruit storage period, resulting in difficult disease management and serious economic losses. Therefore, the characterization of the infection mechanism needs to be explored to deepen our understanding of the pathogen and the disease. In this study, a highly pathogenic strain JY‐1, causing kiwifruit soft rot, was isolated and identified as B. dothidea. A polyethylene glycol‐mediated genetic transformation system for B. dothidea JY‐1 was established, enabling the successful acquisition of a green fluorescent protein (GFP)‐labelled strain with stable inheritance. The GFP‐labelled transformant Bd13 was generated and used in the research, and the infection process of kiwifruit tissues was studied through wound inoculation essays and fluorescence labelling microscopy. The results of the present study indicate that the transformant Bd13 not only damaged the kiwifruit fruits but also effectively infected and colonized the leaves and shoots of kiwifruit plants, causing shoot blight and leaf spot. These findings contribute to a deeper understanding of the pathogenic mechanisms underlying kiwifruit soft rot and lay a foundation for further investigations into the interaction between the soft rot pathogen B. dothidea and kiwifruit.