So I want to get Three Dragon Ante, but I Im going to use it in Third ruleset, I just want to make sure the easier to find 4th Edition Deck could be used with the 3rd Ed rules.
The cards are different, but neither card game interacts* with the RPG rules at all, except at the level of money. Indeed, either can be played all on its own without an RPG involved, so either game will work with either D&D 3.5e or D&D 4e, or really, any other RPG. Played during an RPG, it's just a way to play out an in-RPG gambling event using a separate out-of-RPG game.
The two sets are different and have slightly different rules, but they are compatible:
This game can be played by itself, or in combination with the original Three-Dragon Ante card set. […]
In addition to the added cards and rules, this game also contains complete rules for the original Three-Dragon Ante card game.
An overview of the gameplay (and the details of how the two games are compatible and differ) can be read in this review: “Same Game, Different Thought Process”.
* No interaction in an “outward” direction from cards to the RPG, that is. There were optional rules for the original game that allowed the RPG's mechanics (skills, new feats, and spells) to influence the card game, but there is no reliance upon a particular RPG’s rules built into the card games themselves. Unfortunately, those optional rules are no longer available from that page due yet another WotC website apocalypse.