The invention discloses an improved-particle-swarm-algorithm-based production and transport cooperative scheduling method and system of a supply chain. The method comprises the following steps: step one, setting an algorithm parameter; step two, generating an initial population randomly; step three, carrying out encoding correction; step four, calculating a fitness value and updating a particle velocity and position; step five, carrying out tournament selection; step six, carrying out crossover and variation; step seven, updating the population; and step eight, determining whether a termination condition is satisfied; if so, outputting a global optimal solution; and if not, returning to the step three. Therefore, with consideration of the production and transport cooperative scheduling problem of the distributed storage, an approximate optimal solution is calculated, so that the cost of the supply chain is reduced and the service level of the supply chain is improved.