Basically the south of France is shut down for works over the Ascension weekend (even though popular dates!) and SNCF doesn't care to put replacement options.
There might be one or two daily buses from Perpignan to Montpellier but they'll be overcrowded and you won't be able to board.
(Honestly SNCF would prefer if people drove that weekend lol)
So to put it shortly: your best option is a Flixbus to Montpellier, then a tram/bus combo across the city (easy with some margin) to Sud de Ftance station in the outskirts.
There are a few TGVs from Montpellier Sud de France to Lyon, do not wait to book them.
I'll add an itinerary below for 10th May:
- Flixbus Barcelona - Montpellier-Sabines 07:45 - 12:25 31€ ticket
- tram/bus combo (follow Google Maps or others). It should take under an hour with services every 7-8 min.
- TGV Montpellier Sud de France - Lyon Part-Dieu 14:11 - 15:50 20€ reservation
Really book ASAP whichever option you choose.