I am currently using Houdini 16.0.736, and I have imported a mesh using “File” node and then create a bounding box for it.

But somehow it seems that it is not aligned to the world axis.

The mesh itself is not alighed to the world axis, but it shouldn't affect my bounding box.

This makes my simulation not working. How to handle that, please?

Any chance you could post a HIP file showing the issue? It's very difficult to guess what the issue might be without a file.

If you create a bounding box of a mesh inside an object, at the SOP (geometry) level, it will be axis-aligned in the space of that object, not world space, since all operations on the geometry are in the object's space. Most simulations support object transforms, though, so that should be fine. If your object's transform is identity, world space and the object space are the same, so if you really need the bounding box to be in world space, you can use the Object Merge SOP to transform the mesh into world space, then compute the bounding box. There's probably some way to do it within a single object, using the option to invert the transform, but I haven't thought that through yet.