We'll first prove that the characteristic polynomial of a permutation matrix representing a permutation $\pi\in S_{n}$ having the cycle structure $1^{c_{1}}2^{c_{2}}...n^{c_{n}}$ is of the form $\prod_{j=1}^{n}(x^{j}-1)^{c_{j}}$.
The eigenvalues of any permutation matrix representing the cycle structure $1^{c_{1}}2^{c_{2}}...n^{c_{n}}$ are $i_{th}$ roots of unity counted with multiplicities $c_{i}$ (where i represents the cycle lengths), which is shown here. As we know that Eigenvalues are the roots of characteristic polynomial, the polynomial corresponding to these eigenvalues is clearly $\prod_{j=1}^{n}(x^{j}-1)^{c_{j}}$.
We'll prove that such representation is unique. Before that let's state a fact we'll use
The nth root of unity $\alpha = cos(\frac{2\pi}{n})+isin(\frac{2\pi}{n})$ does not satisfy $x^{k}-1 = 0$ for $0\lt k\lt n$. But for $k\gt n$ it satisfies $x^{k}-1 = 0$ for $k=nt$ where $t\in \Bbb N$.
Coming to the proof, Let $XP_{1}$ and $XP_{2}$ both have same roots of unity counted with multiplicities. But $XP_{1}$ and $XP_{2}$ differ in their representation i.e.
They are like
$$XP_{1} = \prod_{j=1}^{n}(x^{j}-1)^{c_{j}}, XP_{2} = \prod_{j=1}^{n}(x^{j}-1)^{d_{j}}$$ Let $j_{1}$ be the greatest $j$ such that $c_{j}\neq d_{j}$. As per our assumption and the fact we stated above, the occurence of the $j_{1}$ root of unity $\alpha = cos(\frac{2\pi}{j_{1}})+isin(\frac{2\pi}{j_{1}})$ in $XP_{1}$ and $XP_{2}$
$1$. Due to $(x^{j}-1)^{c_{j}}$ for $j\gt j_{1}$ is same in both.
$2$. Due to $(x^{j}-1)^{c_{j}}$ for $j\lt j_{1}$ is zero.
$3$. Due to $(x^{j}-1)^{c_{j}}$ for $j=j_{1}$ viz $c_{j_{1}}$,$d_{j_{1}}$ is different.
But it means multiplicities of $\alpha$ are different in $XP_{1}$ and $XP_{2}$. We reach a contradiction. Hence $c_{j} = d_{j} \space \forall j\in \Bbb N$
Now if two permutation matrices have the same characteristic polynomial they must have the same cycle type and hence they must represent conjugate permutations in $S_{n}$.