So this could be one of the biggest limitations you can run in to when moving your files to SharePoint on line with Office 365
The limitation is with the OneDrive for Business sync client tool. You can actually upload more items than that but if you exceed the sync limit then the sync client tool will stop working. If you still want to use the sync client tool then you will need to split out your files in to separate document libraries. You can do this on your team site and on your OneDrive for Business site – but note that on your OneDrive for Business site only your main document library will be recognized as your default OneDrive for Business library.
for more information about limits of Office 365 see software boundaries and limits