We introduce a stochastic sandwich method with low-mode substitution to evaluate the connected three-point functions. The isovector matrix elements of the nucleon for the axial-vector coupling $g_A^3$, scalar couplings $g_S^3$ and the quark momentum fraction $langle xrangle_{u -d}$ are calculated with overlap fermion on 2+1 flavor domain-wall configurations on a $24^3 times 64$ lattice at $m_{pi} = 330$ MeV with lattice spacing $a = 0.114$ fm.