Good morning Qing,
Great question! Yes, you will need a combined OTU table for these kinds of analysis.
My recommendation is to combine your samples into a single seqs.fna file, directly after demultiplexing (so they have qiime labels) and directly before OTU picking (so that all the samples will end in a single table).
So the process goes like this with a [new step] in the middle:
quality filtering, [ cat sample1.fna sample2.fna sample3.fna > all_seqs.fna ], picking otus, downstream analysis
Let me know if this helps!
P.S. Which OTU picking script did you use? I ask because if you used closed-ref OTU picking, you can merge all your OTU tables using this script.
(Warning: That script only worked with tables make with close-ref OTU picking. If you used denovo or open-ref OTU picking, you cannot merge your OTU tables, because the new OTUs will be different in different tables.)