The incessant advancement of e-commerce has brought promising opportunities for vending fresh commodities and stimulated the ongoing growth in the demand for fresh products. Logistics services serve as a vital link between fresh e-commerce and customers, playing a pivotal role in enhancing customer satisfaction and fostering the sustainable growth of businesses. Therefore, this study endeavors to investigate the correlation between logistics service quality and customer satisfaction within the context of fresh e-commerce, while also identifying the pivotal factors that impact logistics service quality. Initially, a novel logistics service quality measurement scale is developed based on the SERVQUAL model. Then, the study formulates the first hypothesis testing model using customer expectations and perceived value as mediating variables. Subsequently, incorporating the service encounter theory, the constructed logistics service quality measurement factors are re-clustered to establish distinct encounter dimensions and to formulate the second hypothesis testing model, which includes mediating variables of customer emotions and perceived value. Finally, empirical data are gathered and subjected to regression analysis and structural equation modeling to mutually validate both models employing identical input indicators. Results suggest that logistics service quality significantly impacts customer satisfaction across the delineated factors within the five dimensions of the SERVQUAL model, alongside the four aspects of service encounters. Moreover, in the fresh e-commerce sector, customer perceived value, service expectations, and customer emotions play crucial mediating roles between logistics service quality and customer satisfaction. These findings hold practical implications for fresh e-commerce businesses aiming to enhance the service quality of logistics operations and achieve sustainable development in a customer-centric market context.