Kishan I would step back and approach it from a deeper UX perspective; who are your users, what are they doing, what information is pertinent to them?
When you delve a little deeper, the answers might begin to come to the surface.
Thinking through it very quickly and without knowing your users or the context of this expiring card, I'd hazard a guess that your users will rarely need to know the exact second the card is valid for an entire hour out of expiration. They probably don't require such granular information and, like you've discovered, it becomes messy and a little confusing when you try to format it.
Perhaps the user only needs to see the seconds in the last 10 minutes, 5 minutes or 1 minute, much like the countdown of an Ebay item, once you hit the hour it could be minute based (58 minutes remaining) then when you hit the sweet spot, it changes colour/state and gets down to detail; 2 minutes 33 seconds remaining.
Worth a think through from your users perspective and what the countdown timer is actually trying to achieve; sales/bonus information/urgency etc?