Non-leading contribution to the pion electromagnetic form factor which comes from the pion twist-3 wave function is analyzed in the modified hard scattering approach (MHSA) proposed by Li and Sterman. This contribution is enhanced significantly due to bound state effect (the twist-3 wave function is independent of the fractional momentum carried by the parton and has a large factor $\sim m_\pi^2/m_0$ with $m_\pi$ being the pion meson mass and $m_0$ being the mean u- and d-quark masses). Consequently, although it is suppressed by the factor $1/Q^2$, the twist-3 contribution is comparable with and even larger than the leading twist (twist-2) contribution at intermediate energy region of $Q^2$ being $2 \sim 40 {GeV}^2$.