The road network in rural areas is complex and the infrastructure is relatively backward. The multi-temperature zone cold chain logistics involves agricultural products with different temperature requirements, which requires considering the transportation cost, carbon emission cost, refrigeration cost, and time cost of different temperature zones during path planning, thereby increasing the difficulty of path planning. Therefore, a multi-objective optimization-based algorithm for selecting the optimal path of rural multi-temperature zone cold chain dynamic logistics intermodal transportation is proposed. Based on the analysis of the multi-temperature cold chain collection and distribution model based on multimodal transportation, a multi-objective optimization model is constructed. This model aims to minimize transportation costs, carbon emission costs, refrigeration costs, time costs, and maximize logistics quality, while satisfying constraints such as transfer schedule times, the number of transport mode conversions, transport mode selection, and time continuity. To solve this model, an improved NSGA-II algorithm is adopted, which combines an improved mutation operator, congestion distance calculation, and the C-W saving algorithm to achieve the optimal transport path solution. Additionally, ArcGIS software is used to implement the shortest path planning based on real road networks. The experimental results show that by selecting the road-rail combined transport mode and adopting the D1–D6–D10 transport path, it is possible to transport fresh agricultural products from location A to the distribution center at location B, with the lowest Pareto fitness value. Furthermore, the algorithm's effectiveness is further verified by completing the end-of-life fresh agricultural product distribution task with four multi-temperature refrigerated vehicles. The study also finds that extending or shortening the latest service time window for customers, although it leads to a decrease or increase in the optimal value of the algorithm's objective function, has little impact on the average distribution time and transport vehicles. These findings provide new theoretical and practical guidance for the path selection of multimodal transportation in multi-temperature cold chain logistics, with significant theoretical and application value.