Short answer: yes—you can animate a mesh with clips that live in a different FBX. The animation does not have to be baked into the same file, as long as the rigs are compatible.
Here’s how it breaks down:
- Import your mesh FBX and set Rig > Animation Type = Humanoid. Let Unity Create Avatar.
- Import the animation FBX(es) and also set them to Humanoid.
- Put the clips from the animation FBX into an Animator Controller on your mesh.
- Unity will retarget the motion via the Avatar, so the source and target can be different models, sizes, and proportions.
- Tips:
- If poses look off, open Configure… to fix bone mapping & T-pose.
- For root motion, ensure the clip’s Root Transform settings and the source rig’s Root node are correct.
- Import both FBXs with Rig > Animation Type = Generic.
- The skeleton hierarchy and bone names must match (or be very close).
- In the animation FBX, you can set Avatar Definition = Copy From Other Avatar and reference the mesh FBX’s avatar so Unity knows the same skeleton layout.
- Drop the clips into the Animator on the target. If the hierarchies differ, retargeting won’t work cleanly.
- Possible but deprecated. Prefer Animator/Humanoid or Generic.
- Clips can animate blend shapes even from another FBX, but the blend shape names must match the target mesh’s names.
- Mesh FBX: set Rig (Humanoid/Generic), Create Avatar.
- Animation FBX: set same Rig type (Humanoid is most flexible).
- Drag the animation clips from the animation FBX into an Animator Controller on the mesh’s Animator component.
- Adjust Root Motion and Avatar Masks as needed.
So: keep animations in separate FBX files—totally fine—and let Unity’s Avatar system (Humanoid) or matching skeleton (Generic) do the work.