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It sounds like a bag of lose metal, but it only happen on certain rev range( around 3k) under heavy load, or lift off the throttle on higher rev range , it will go away when the clutch is not engage , but I'm quite sure it's nothing to do about the clutch.

Anyone have any clue about what it is ???

Drain the the diff oil.
Noise can be a miss leading, I could of swore I blew the gear box in my Rx7. Only to pull it out and strip it, to find nothing wrong with it.
Diff oil, had a lovely chunks of metal in it.

I.E. check the easy stuff first.

Diff oil had change not long ago and it seems ok.....
Is there any possibility that it's the worn out bearing ?

Jack the car up.
Remove the stub axles, drive shaft. Drain the oil.
Remove the diff and have a look. It's really the only way to tell for sure. Removing the diff is easier than the gear box.
Bright side is the MX5 is bloody easy to work on.

If there is metal in the diff then something has failed. Diffs are a specialist area- just go to a transmission specialist and get them to check or listen for pointer on the problem. If unconvinced read a workshop manual and decide if you are prepared to take the work on and have the time and resources.

Thanks for the advise guys , will jack it up when I have some spare time.

Looks like its running ok, but just the noise that bothers me a lot =[

echoing Mr Morlock.

Take it to a shop if you're intending to open the diff.

Replacing a centre is not a home job, you need specialist equipment to correctly set the backlash etc for the Crown and Pinion.
If not set correctly, the diff may chew itself apart.