A novel oil storage method utilizing flexible oil bladders to store oil in waters is proposed. The proposed method has the advantages of conserving land resources and economic cost, high fire and explosion protection performance. And it does not require an oil-water displacement method. However, the application of the proposed method is severely limited by oil pollution. To overtake the limitation, the permeation-diffusion combination action mechanism of flexible oil storage in waters is investigated. The analytical solution of oil concentration distribution in water under the permeation-diffusion combination action is presented, of which the accuracy is verified by model experiment and numerical simulation. The results indicate the oil concentration in water can quickly reach a stable value that is directly proportional to the oil permeation rate of membrane material. Simultaneously, the oil permeation rate standard of ellipsoid bladder is suggested to be 1.436 × 10−6g/m2s and the interval between oil bladders is set at 1.5 times of the bladders diameter. Furthermore, a relationship equation has been given between the thickness of membrane and oil permeation rate. This study offers theoretical and engineering guidance for the application of flexible oil storage in waters and has certain significance for the development of underwater oil storage.