A large amount of raw nanomaterials is processed with the increasing demand of fishery products. Membrane technology and bioprocessing have been increasingly involved in fishery industry, particularly for the treatment of fishery wastes. Fishery nanowastes including both solid and liquid contain high content of organic compound which may cause the pollution to the environment. Membrane technology could recover valuable nanocompounds back from fishery nanowastes, therefore not only it will reduce the risk of pollution but also improve economic benefit of fishery industry. Comparing to other competing methods, membrane technology serves as a simple, large scale and mild method to achieve both high efficiency and maximum preservation of natural property of recovered compounds. A series of valuable biomolecules such as protein, enzymes, collagen and marine flavor could be recovered from fishery byproducts by membrane technology. Different membrane processes mostly microfiltration, ultrafiltration, reverse osmosis and nanofiltration have been employed followed by protein SDS gel electrophoresis at different temperatures, pH and ionic concentrations. These membrane processes could work individually or be combined with other biochemical reactions to develop a hybrid multistage membrane process for the desirable recovery rate, high purity of recovered compound and development of new product. The performance of these processes could be improved by model design or other additional techniques such as ‘gas sparging’. In addition to recovery of valuable compounds, membrane process has also been applied for treatment of both fish pond and fishing process water to achieve water recycle. In the future, more industrial success of membrane technology in fishery industry is expected.