The invention provides a terrain-matching navigation filtering method of an AUV. The method comprises the following steps: estimating terrain matching and positioning errors, correcting a terrain matching and positioning likelihood function, estimating a terrain matching and positioning confidence interval, and fusing and filtering reference navigation and terrain matching results. The method mainly comprises a method for estimating terrain matching and positioning errors and a method for fusing terrain matching and positioning data with reference navigation data. According to the terrain-matching navigation filtering method, a terrain-matching navigation computer is used for receiving reference navigation data and real-time terrain measurement data; positioned positions can be estimated by two steps of matching and positioning, fusing and filtering; then position information is transmitted to a reference navigation computer and is used for correcting navigation; and continuous recursive navigation can be achieved.