The descent camera mounted on the CE-5 lander captured abundant images during the landing, which can be used to generate local terrain models with details from sub-meter to millimetre scales. But unlike Earth, high-precision control data are unavailable on the Moon especially for small regions like the landing sites, making it hard to define exact geo-reference of the local terrain models, which is essential for topographic and geomorphological mapping and analyses. To tackle this problem, this paper proposes a method for geo-referencing free 3D models generated from the CE-5 descent images based on low-resolution geo-referenced orbiter data. On account to the large discrepancy between the accuracies in the horizontal and vertical directions of orbiter data, the proposed method used two independent alignments in 3D and 2D spaces respectively to reduce the impacts of accuracy unevenness of the reference data. The 3D alignment is performed based on mass features to align the base-plane of the free model, and the 2D alignment is performed based on matched point features projected on the base-plane to define the scale and orientation of the model. After these the alignments, the free model is ultimately enriched with geo-reference information and used to generate fine-scale DEM and DOM of the CE-5 landing site. The average horizontal distance between the referenced data and the geo-referenced data is 2.19 m with a small standard deviation of 1.48 m, and the average height difference between the generated DEM and the reference DEM is 2.78 m, indicating a reliable 3D geo-referencing result.