The present invention belongs to the technical field of petroleum exploitation engineering, and discloses a 3D modeling method for pore-filling hydrate sediment based on a CT image. Indoor remolding rock cores or in situ site rock cores without hydrate can be scanned by CT; a sediment matrix image stack and a pore image stack are obtained by gray threshold segmentation; then, a series of pore-filling hydrate image stacks with different saturations are constructed through image morphological processing of the pore image stack such as erosion, dilation and image subtraction operation; and a series of digital rock core image stacks of the pore-filling hydrate sediment with different saturations are formed through image subtraction operation and splicing operation to provide a relatively real 3D model for the numerical simulation work of the basic physical properties of a reservoir of natural gas hydrate.