Abstract: The raw side-scan sonar images are sequenced by scan line,and have not holistic geographical positioning and scalability. The original side-scan sonar image can't be analysed and used until it has been geocoded with geographical references. However,the geocoded images would have gaps after geographical positioning. This paper investigates the factors which cause the gaps in the process of geocoding. A practical navigational processing model based on navigation files is proposed in the paper. The model has been applied in sonar image processing system(GeoSonar) to process side-scan image in Hangzhou Bay,which proves the method effectiveness.