Automated picking system such as A-frame has been used widely for the distribution center to quickly fulfill a lot of broken-case orders because of its high efficiency, high accuracy and low labor costs. While in practice, it is a key problem in the distribution center design to how to choose an order fulfillment strategy for the given item between manual picking and automated picking from a cost perspective, and how to assign items between manual picking zone and automated picking zone. By analyzing labor costs in these two zones, a math model for the allocations of equipment channels is established. The objective function is the sum of total labor savings. A greedy algorithm is proposed to solve how many channels are allocated to each item in the automated picking zone. Based on this, the problem is generalized into the items assignment for double picking zones with manual picking and automated picking system. It can be classified as a type of special knapsack problem, and a heuristic algorithm is adopted to solve it. The example simulation for the pharmaceutical distribution center proves the effectiveness of the algorithms.