The homogeneous coordinate ring of a projective variety is not invariant under isomorphism.
For example I was taking let $X = \Bbb P_1$, and let $Y$ be the $2$-uple embedding of $\Bbb P_1$ in $\Bbb P_2$. Then $X\cong Y$. But show that $S(X)\ncong S(Y)$.
Now I can embed $\Bbb P^1$ in $\Bbb P_2$ s.t $[x_0,x_1] \to [x_0^2,x_0x_1,x_1^2]$. Now what I see that $V([x_0,x_1])=\{(0,0)\}$ and $V([x_0^2,x_0x_1,x_1^2])=\{(0,0,0)\}$.
So am I going in a right way? Because I am not getting how to get $X$ and $Y$ and how to arise in $S(X)\ncong S(Y)$?