The world famous bay areas’ various development patterns are especially important for Shenzhen，a city with the emergence of development pattern of bay area economy，to find suitable reference. This paper，based on the geographic locations and development histories of San Francisco and Shenzhen，states the similarities of the bay area economies of the two cities during the formation process. Then，this paper makes deep comparison on the competitive industries，city orientation，atmosphere for innovation，research and development conditions of San Francisco and Shenzhen，and further puts forward that San Francisco Bay Area is the best reference for Shenzhen to develop bay area economy and to draw on the experience of San Francisco，and finally，this paper make good suggestions for the development of Shenzhen bay area economy.