Location and navigation technologies are the key of autonomous ship in lakes. This paper establishes an autonomous ship navigation system, designs the global static coordinate and the local static coordinate, the ship dynamic coordinate and kinematics model. According to human driving technologies, a cruise navigation mode is designed and a region navigation mode is given for saving energy, and navigation strategies using if-then rules. Reasons of practical measurement location data noises of GPS and electronic compass are analyzed. In order to improve the precision of location, FIR digital filtering is designed using Hamming window function. Monitoring area calculating equation is derived. Navigation algorithms and interfaces are programmed based on VC++. And navigation experiments are accomplished on self-developed autonomous ship. Results show that effect of FIR filtering to electronic compass is better than to GPS signals, and the cruise mode can achieve a wide range of scanning and monitoring and the given region mode can achieve the monitoring of key areas using lesser energy consumption.