In this paper, we consider the following fractional Schrödinger-Poisson system with critical exponent \(\begin{aligned} {\left\{ \begin{array}{ll} (-\Delta )^s u+V_{\lambda } (x)u+\phi u=|u|^{2_s^*-2}u+f(u), & ~\textrm{in}~~\mathbb {R}^3, \\ (-\Delta )^t \phi =u^2, & ~\textrm{in}~~\mathbb {R}^3, \end{array}\right. } \end{aligned}\) where \(s\in (\frac{3}{4},1), t\in (0,1)\) , \(2_s^*:=\frac{6}{3-2s}\) is the fractional critical exponent, \(V_{\lambda }(x)\) = \(\lambda V(x)+1\) with \(\lambda >0\) . Under some suitable assumptions on f and V, if \(\lambda >0\) is large enough, we prove the existence of ground state sign-changing solutions for the above system by using the constraint variational method and the quantitative deformation lemma. Moreover, the least energy of sign-changing solution is strictly more than twice the energy of the ground state solution. At the same time, we also study the asymptotic behavior of ground state sign-changing solutions as \(\lambda \rightarrow \infty \) . Our results improve the recent results in the literature.