Suppose that $\mathcal{M} \preccurlyeq \mathcal{N}$. Then by definition we have that $\mathcal{M}$ is a substructure of $\mathcal{N}$ s.t. for any (possibly empty) tuple $\overline{a}$ from $M^n$ and for any $\phi \in L$, we have that $\mathcal{N} \models \phi(\overline{a})$ implies that $\mathcal{M} \models \phi(\overline{a})$.
Now we aim to show that $\mathcal{M} \equiv \mathcal{N}$. This is true iff $Th(\mathcal{M}) = Th(\mathcal{N})$. I can only think of how to show that $Th(\mathcal{M}) \supseteq Th(\mathcal{N})$. This is done as follows: let $\phi \in Th(\mathcal{N})$. Then for any tuple $\overline{a} \in M^n$, we have that $\mathcal{N} \models \phi(\overline{a})$. Among these tuples are the empty tuple, so that we can say
$$ \mathcal{N} \models \phi() $$
so that of course
$$ \mathcal{N} \models \phi $$
and hence applying the definition of $\preccurlyeq$ we get:
$$ \mathcal{M} \models \phi() \implies \mathcal{M} \models \phi $$
Then we've established that $Th(\mathcal{N}) \subseteq Th(\mathcal{M})$. But how do we show that $Th(\mathcal{M}) \subseteq Th(\mathcal{N})$?
Suppose $\phi\in\text{Th}(\mathcal{M})$. Then $\lnot\phi\not\in\text{Th}(\mathcal{M})$. So by your argument, $\lnot\phi\not\in\text{Th}(\mathcal{N})$, and hence $\phi\in\text{Th}(\mathcal{N})$.
More generally, if $T$ and $T'$ are complete theories, then $T\subseteq T'$ implies $T = T'$.
Comment: The definition of $\preccurlyeq$ is often taken to be $\mathcal{N}\models \phi(\overline{a})$ if and only if $\mathcal{M}\models\phi(\overline{a})$, for $\overline{a}$ from $\mathcal{M}$. This is equivalent, of course.