Abstract: The invention relates to a separating system with hollow fiber membranes and an operating method. A dual backwash loop which is a pipeline connecting a top port of the said membrane assembly to a cleaning pump through a first branch and a second branch. The first branch is designed to fill a small amount of cleaning liquid into the said membrane assembly; and the second branch is designed to fill a relatively large amount of cleaning liquid in order to clean the membrane adequately. The said system operates in the following procedures: operation status, cleaning status 1, cleaning status 2, drain status, returning to the operation status. The technology of the present invention may be used to enhance the cleaning effect to the membrane system, further save water for the cleaning process, shorten the cleaning time, thus benefiting the continuous large scale industrial production and having higher efficiency.