In this paper,studying the problem of hypersonic ballistic missile attacking large moving target on the sea and considering the motion characteristic of the target,we focus on the passive tracking subject of height-measurable missile.In terminal guidance of hypersonic ballistic missile,measurement noise of LOS (line-of-sight) angle which is provided by infrared seeker is large due to aerodynamic heating effect.Inaccuracy of the measured information will result in slow convergence of the filter or even divergence.Meanwhile,due to poor system observability,relative velocity needed by a precise guidance law cannot be accurately estimated.Existing high-precision GPS/INS(Global Positioning System / Inertial Navigation System) integrated navigation system can provide location information of the missile itself.Considering this advantage of GPS/INS integrated navigation system and targets motion characteristic of moving in two-dimensional horizontal plane,we rebuild the filter equation for the missile and the target using height information of high accuracy and angle information with certain level of noise to be measurable information.Introduction of height information improves observability of the filter equation.Hence relative velocity and precise LOS angle as well as LOS rate from the missile to the target can be estimated.Simulation is given to verify the stability,accuracy and effectiveness of the filter system.