We deal with the design of the effective block logistics operating system in shipyard. The block logistics operation is one of the critical managerial problems in shipbuilding. The block logistics operation in shipyard consists of storage operation for temporary storage in the limited storage area and transfer equipment operation of blocks from the given storage area to next process according to the block production schedule. We propose a design method of block logistics operating system based on the axiomatic design and IDEF0 method. As a result of axiomatic design, system functions are determined regarding implementation sequence. We validated the proposed design by implementation of a block logistics operating system for a large scale shipyard.