At present, the pharmaceutical logistics industry in our country is still not perfect, and the pharmaceutical logistics enterprises have not occupied the home of advantage in China. Establishing pharmaceutical logistics distribution center can make well coordination with production, transportation and other aspects, so that the upstream and downstream enterprises can complete the delivery mission, shorten the logistics time, reduce logistics cost better. The actual data of import goods in this paper to Zhongyou of pharmaceutical logistics company in Gansu at present as the basis, use the association graph method to design the best layout of distribution center, draw the final layout, make reasonable arrangements for each functional area location, shorten the walking path, improve the distribution center operation efficiency, so as to provide quality service delivery for each customer, in order to meet the needs of daily doses of whole northwest area.