In view of antinomy between the logistics service quality and the logistics cost of the supply chain, this paper analyzed the related logistics service quality objectives and logistics cost targets of the core manufacturing of the manufacturing supply chain, and the upstream and downstream nodes enterprises respectly in the procurement, production, transportation, inventory, sales and other areas. Then this paper planed the service quality objectives and cost targets of the supply chain logistics system, and then established the multi-objective programming model. Thus the supply chain logistics system will reach equilibrium between logistics service quality goals and objectives of the logistics costs. And then supply chain logistics system will achieve the overall best economic interests.