I have used CloudKit in my app, but it had been rejected by Apple with reason because of CloudKit not work, but I have tested that build via TestFlight and it's worked in my end. Any body faced this issue and any advice for me? Thanks.
There are a lot of possible variants about why your application is being rejected. In iTunes Connect I would ask Apple Review Team about more details. And then please update your question if you could not solve it alone.