A hybrid-computing navigation system worn by a user includes a modified motion sensor group which includes 9-axis or 10-axis motion sensors that are built-in, and a host device configured for providing navigation information, in which the modified motion sensor group is worn on the user so that a moving direction of the user is the same as a heading direction calculated from the modified motion sensor group. The modified motion sensor group provides step counting and absolute orientation in yaw, roll and pitch using a sensor fusion technique. The navigation system further includes at least one wireless sensor at wifi hot spot to perform sensor fusion for obtaining an absolute position of an estimated position of the user. Sensor fusion combining with location map are used to perform location map matching and fingerprinting. A method of position estimation of a user using the navigation system is also disclosed.