Let $\mathscr{P}$ be a symplectic polar space over a finite field $\mathbb{F}_q$, and $\mathscr{P}_m$ denote the set of all $m$-dimensional subspaces in $\mathscr{P}$. We say a $t$-intersecting subfamily of $\mathscr{P}_m$ is trivial if there exists a $t$-dimensional subspace contained in each member of this family. In this paper, we determine the structure of maximum sized non-trivial $t$-intersecting subfamilies of $\mathscr{P}_m$.