Logical order is the ordering of the index. Let's assume an index based on last name. The logical order would be:

Adams

Johnson

Smith

Williams

But, due to page splits, insertions, deletes and the other things that can affect the order in which pages or stored, the physical order, meaning the order of the actual storage, may look like this:

Adams

Wiliam

Johnson

Smith

Defragmenting will move the order of the physical storage closer to that of the logical definition. It may not be exact and it's unlikely to remain so as the data changes.