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The time-dependent vehicle routing problem of time windows of fresh agricultural products distribution have been studied by considering both economic cost and environmental cost. A calculation method for road travel time across time periods is designed in this study. A freshness measure function of agricultural products and a measure function of carbon emission rate are employed by considering time-varying vehicle speeds, fuel consumptions, carbon emissions, perishable agricultural products, customers’ time windows, and minimum freshness. A time-dependent green vehicle routing problem with soft time windows (TDGVRPSTW) model is formulated. The object of the TDGVRPSTW model is to minimize the sum of economic cost and environmental cost. According to the characteristics of the model, a new variable neighborhood adaptive genetic algorithm is designed, which integrates the global search ability of the genetic algorithm and the local search ability of the variable neighborhood descent algorithm. Finally, the experimental data show that the proposed approaches effectively avoid traffic congestions, reduce total distribution costs, and promote energy conservation and emission reduction.