For getting more exact vertical acceleration information and improving the altitude estimate, an altitude measure system for unmanned helicopter with high precision is presented based on the barometric altitude sensor, GPS and strapdown accelerometer. After analyzing the sensors’ factors, state equation and measuring equation of the system are established according to kinematics and sensors measuring principle of certain unmanned helicopter and noise drowned technology. Using central kalman filter is used to estimate the altitude and full digitized simulation experiment is carried out of the unmanned helicopter. Simulation results show that altitude measurement of the system can give more accurate estimation than one sensor.