For anyone wishing to take a bus from Krabi to Hat Yai for onward travel to Malaysia, this is the recent journey I made in August 2017. I went all the way to Penang but you can catch trains to other destinations like KL at Padang Besar train station.
You catch a Songthaew from the main road next to the river to Krabi bus station - 20 baht (I think locals pay 10-15 baht from the town but my guy negotiated. It's 60 baht from Ao Nang)
Big bus from Krabi bus station to Hat Yai Terminal 1 takes 5 hours and leaves every hour starting at 8.30am - 214 baht- toilet on the bus and 10 mins lunch break in Trang
Minivan from Hat Yai bus terminal 1 from stand 24 leaves when full and takes 1 hour - 50 baht for one ticket. They will make you pay an additional ticket for your bag to occupy a seat otherwise you have to carry it on your lap. Alternatively you can get a government bus for 44 baht from the town outside the clock tower leaving every hour.
The minivan drops you right outside thai immigration control so get your stamp out. Then you walk 10 mins to Malaysian immigration to get your stamp in. Walk another 5 mins to the train station.
Train from Padang Besar to Butterworth leaves 25 mins past every hour and takes 2 hours. Cost 11.40 MYR for one person.
From Butterworth you walk 5 mins to the ferry and pay 1.20 MYR for one person for a 15 mins ride. Ferries leaves every 20-30 mins.
All in all we spent the equivalent of 350 baht and the journey took us 12 hours. The travel agent in Krabi offered us a tourist bus/mini van for 750 baht which she was selling 9 hours.
Getting the mini van at Hat Yai to Padang Besar was stressful and I argued with the guy over space for my bag but once we set off it was ok. The journey was really smooth especially once we crossed over to Malaysia. Everything was sign posted, people pointed us in the right direction and no one tried to scam us out of any money.
Great journey 👌🏼Let me know if you have any q's