Isomorphism notion between sets of triples Graph Isomorphism is natural problem which is most widely believed to have intermediate complexity between $P$ and $NP$-complete. GI can be thought as deciding the existence of an isomorphism between two sets of node pairs. I'm trying to develop a notion of isomorphism between sets of triples. 

We are given two hyper-graphs $G1$ and $G2$ such that the set of hyperedges ($E_1$ and $E_2$) consists of  triples of 3 nodes $\{t_1, t_2, t_3 \}$. We say that Hyper-graphs $G1$ and $G2$ are isomorphic if there is bijection $f$ from $V_1$ to $V_2$ such that pair $\{u,v\} \in E1 $ if and only if $\{f(u),f(v) \} \in E2 $. We say $\{u, v \} \in E $ if there is a triple (hyperedge) $\{ u, v, z\} \in E$ for some node $z$.   

Is it $NP$-complete to decide the existence of such isomorphism between two hyper-graphs $G1$ and $G2$?
Your problem reduces to graph isomorphism, so is not $\mathsf{NP}$-complete unless the polynomial hierarchy collapses. 

In fact, you've essentially already given the reduction in your question: given a 3-uniform (=every hyperedge has size 3) hypergraph $G$, construct from it the graph $f(G)$ which has the same vertex set, and such that $\{u,v\} \in E(f(G))$ iff there exists a $z \in V$ such that $\{u,v,z\} \in E(G)$. (When $G$ is a hypergraph, I use $E(G)$ to mean the set of hyperedges.) Then $G_1$ and $G_2$ are isomorphic-in-your-sense iff $f(G_1) \cong f(G_2)$ as graphs. It is not hard to check that this reduction only takes polynomial time (note that $|E(f(G))| \leq |V(G)| |E(G)|$). 

It is also probably worth mentioning that there is already a well-established notion of hypergraph isomorphism that is different from your notion. If we consider a hypergraph $G$ as a vertex set $V$ together with a collection of hyperedges $E \subseteq P(V)$ (each hyperedge is a subset of $V$), then two such hypergraphs are isomorphic if there is a bijection $\pi\colon V_1 \to V_2$ such that $E_2 = \pi(E_1)$. (Here I am abusing notation twice: by "$\pi(E_1)$" I mean $\{\pi(e) : e \in E_1\}$ and by $\pi(e)$ for $e \subseteq V$ I mean $\{\pi(v) : v \in e\}$.) Hypergraph isomorphism in this sense is Karp-equivalent to graph isomorphism, but by a slightly less immediate reduction than from your problem. However, fast (in theory) algorithms for hypergraph isomorphism are often more difficult than those for graph isomorphism (see, e.g. Babai and Codenotti, FOCS 2008).