Two permutations are conjugate of each other if and only if they have the same cycle structure.
If I want to find the number of elemnts in $S_{13}$ that are both conjugate to (123)(45) and (12)(34), then is the answer 0? because (12)(34) and (123)(45) have not got the same cycle structure.
That is correct. For this example, also notice that the two elements you mention have different orders. $(12)(34)$ has order 2 while $(123)(45)$ has order 6.
Given a group $G$ suppose that $a,b\in G$ are conjugate. Then there exists $c\in G$ such that $cac^{-1}=b$. If $a$ has order $n$, that is if $a^n=e$, then $$b^n=\left(cac^{-1}\right)^n=cac^{-1}cac^{-1}\cdots cac^{-1}=ca^nc^{-1}=cc^{-1}=e$$ so that $\text{ord}(b)\leq \text{ord}(a)$. By symmetry, we also have that $\text{ord}(a)\leq \text{ord}(b)$ and hence $\text{ord}(a)=\text{ord}(b)$.