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So, in order to proceed with export urdf, should I add reference coordinate system and axis mannually for model?

If you want to have joints in your exported URDF: yes.

If so, it is a pretty time-cosuming, in other words, using original assembly file which contains assembly relation is the correct way to export urdf. Am I right?

That would certainly seem to be the most straightforward way of doing it, yes.

However, exporter plugin might be only fit to SW2012, original assembly is built in newer version.

I would try the plugin with a newer version of SW. It can work, it's just not supported / recommended.