We study the partial regularity problem for a three dimensional simplified Ericksen-Leslie system, which consists of the Navier-Stokes equations for the fluid velocity coupled with a convective Ginzburg-Landau type equations for the molecule orientation, modelling the incompressible nematic liquid crystal flows. Base on the recent studies on the Navier-Stokes equations, we first prove some new local energy bounds and an ε-regularity criterion for suitable weak solutions to the simplified Ericksen-Leslie system, i.e., for σ ∈ [0, 1], there exists a ε > 0 such that if (u, d, P ) is a suitable weak solution in Qr(z 0 ) with 0 < r ≤ 1 and z 0 = (x 0 , t 0 ), and satisfiesHere, H −σ (Br(x)) is the dual space of H σ 0 (Br(x)), the space of functions f in the homogeneous Sobolev spaceḢ σ (R 3 ) such that supp f ⊂ Br(x). Inspired by this ε-regularity criterion, we then improve the known upper Minkowski dimension of the possible interior singular points for suitable weak solutions from 95 63 (≈ 1.50794) given by [24] (Nonlinear Anal. RWA, 44 (2018), 246-259.) to 835 613 (≈ 1.36215).