Mechanisms of scale effect on water saving irrigation and non-point source pollution were analyzed. Because of scale effect, field scale can't be used as a substitute for irrigation system scale, and irrigation system scale was too complex for study, therefore, the concept of small watershed of irrigation system (SWIS) was defined. Being the basal ecology unit of irrigation system, SWIS was also an aggregation of a number of fields, a much smaller scale unit. Feasibility and significance of water saving irrigation and non-point source pollution management in SWIS were demonstrated, and then comments and opinions were brought forth on contents and methods of studies on water saving irrigation and non-point source pollution management in SWIS.