The work aims to optimize and coordinate the relationship between inventory replenishment and distribution in the secondary supply chain system involving 3rd Party Logistics under VMI and reduce the inventory and transportation costs of the system while ensuring the distribution needs of retailers. The factors such as the transportation distance of fresh products in the inventory routing system under the 3PL logistics model, the time window of freshness quality, and the adjustment of the distribution and the inventory cost of each retailer were considered comprehensively. Then, a multi-variety fresh product inventory routing optimization model was established with the fuel cost of heterogeneous fleet vehicles, the fixed cost of vehicle dispatch, the cost of delivery overtime and the inventory cost of each retailer as objective functions. The improved genetic algorithm was used to optimize and adjust the distribution volume and obtain the final fresh product distribution scheme. The total cost was reduced by 9.98% compared with that before the distribution volume adjustment. Splitting and adjusting the distribution volume in time can save the total cost of the supply chain system.