I think this may be the parents of your John (as already given by Osprey)
1861 Wales census
Glamorgan, Ystraddyfodwg, Treherbert
Benj JONES 40, smith, b Glamorgan
Dinah JONES 33,
b Llanfwrnach,William JONES 3, b Glamorgan Ystrad
Elizabeth JONES 8 months, b Glamorgan Ystrad
Unfortunately there are too many John JONES registered in Merthyr Tydfil in 1863 to have any hope of finding exactly which one is yours.
Continuing on from this - on another thread you thought his mother's surname may have been
NICHOLESS OR MOHOLESS??1851, Glamorgan, Aberdare, Llwydcoed
John Nicholas 61, labourer
Mary Nicholas 60
Benjamin Nicholas 25
John Nicholas 18
Dinah Nicholas 22 b Llanfwrnach, Pembrokeshire, Wales
Thomas Nicholas 8
Margret Nicholas 5
David Edmunds 11 Mo
Henry Phillips 24
There is an online tree which suggests that these two census entries are the correct family. However, there is no documentary evidence cited, nor can I see a marriage for Benjamin Jones and Dinah Nicholas. The tree does give John's name as the couple's third child also b Ystraddyfodwg, 1862.
The tree owner's profile says she lives in Aberdare so she may have good access to local records.
Sometimes the Welsh place names can be helpful - having Dinah's birthplace with it's unusual spelling has been very handy!
I'm happy to type up more but it's way past the witching hour here.
Will return tomorrow.
Judith