Artificial reefs are basic fishery facilities for marine habitat conservation and construction. In order to enhance fishery resources and restore the ecological environment in Laizhou Bay, where is an important fishing ground in China, an assembly-type oyster reef was designed based on the biological community, water depth and sea current in Laizhou Bay. This paper studied the effect of filling oyster shell in the assembly-type oyster reef on the flow field distribution by computational fluid dynamics (CFD), optimized the structure of reef, and presented the construction deployment of reef habitat and assessed potential of carbon fixation of oyster reefs. Indexes of upwelling, slow flow and vortex were chosen to describe the flow field effect of oyster reefs. The distribution characteristics of flow field under three types of filling oyster shell were analyzed: filling no shell (UAR), filling shells with an 83.6 void ratio (OAR), and filling shells with a 0 void ratio (FAR). The results showed that the upwelling, vortex and slow flow efficiency indicators of the OAR had obvious advantages compared with the other two filling methods, and the efficiency indicators of OAR with the spacing between basic elements of 280 m and deployment angle of 0° were higher than the others. Finally, according to the study result of filling method, spacing and deployment of oyster reef, the assessment showed that reefs could fix 2178.9 t carbon by themselves on the basis of national marine ranching demonstration area regulations in China.