Community retail is an important research issue in the field of fresh agriproduct e-commerce. This paper focuses on the problem of last-mile multi-temperature joint distribution (MTJD), which combines time coupling, order allocation, and vehicle scheduling. Firstly, according to the temperature of a refrigerated truck in multi-temperature zones, a split-order packing decision is proposed to integrate the different types of fresh agriproduct. Then, the order allocation strategy is incorporated into a comprehensive picking and distribution schedule, while taking into account the time-coupling of picking, distribution, and delivery time limit. To improve consumer satisfaction and reduce order fulfillment costs, an optimization model combining multi-item order allocation and vehicle scheduling is established, to determine the optimal order allocation scheme and distribution route. Finally, taking fresh agriproduct community retail in the Gulou District of Nanjing as an example, the effectiveness and feasibility of the model are illustrated. The numerical results of medium- to large-scale examples show that, compared with the variable neighborhood search algorithm (VNS) and genetic algorithm (GA), the mixed genetic algorithm (MGA) can save 29% of CPU time and 65% of iterations. This study considers the integrated optimization of multiple links, to provide scientific decision support for fresh agriproduct e-commerce enterprises.