A type of charged phospholipid polymer biointerface was constructed on a quartz microfluidic chip to control the electroosmotic flow (EOF) and to suppress non-specific protein adsorption through one-step modification. A negatively charged phospholipid copolymer containing 2-methacryloyloxyethyl phosphorylcholine (MPC), n-butyl methacrylate (BMA), potassium 3-methacryloyloxypropyl sulfonate (PMPS) and 3-methacryloxypropyl trimethoxysilane (MPTMSi) moieties (referred to as PMBSSi) was synthesized to introduce such phosphorylcholine segments as well as surface charges onto the silica-based microchannels via chemical bonding. At neutral pH, the homogenous microchannel surface modified with 0.3 wt% PMBSSi in alcoholic solution, retained a significant cathodic EOF ((1.0 ± 0.1) × 10−4 cm2 V−1 s−1) with approximately one-half of the EOF of the unmodified microchannel ((1.9 ± 0.1) × 10−4 cm2 V−1 s−1). Along with another non-charged copolymer (poly(MPC-co-MPTMSi), PMSi), the regulation of the surface charge density can be realized by adjusting the concentration of PMBSSi or PMSi initial solutions for modification. Coincidently, the ζ-potential and the EOF mobility at neutral pH showed a monotonically descending trend with the decrease in the charge densities on the surfaces. This provides a simple but feasible approach to controlling the EOF, especially with regard to satisfying the requisites of miniaturized systems for biological applications requiring neutral buffer conditions. In addition, the EOF in microchannels modified with PMBSSi and PMSi could maintain stability for a long time at neutral pH. In contrast to the EOF in the unmodified microchannel, the EOF in the modified microchannel was only slightly affected by the change in pH (from 1 to 10). Most importantly, although PMBSSi possesses negative charges, the non-specific adsorptions of both anionic and cationic proteins (considering albumin and cytochrome c, respectively, as examples) were effectively suppressed to a level of 0.15 µg cm−2 and lesser in the case of the 0.3 wt% PMBSSi modification. Consequently, the variation in the EOF mobility resulting from the protein adsorption was also suppressed simultaneously. To facilitate easy EOF control with compatibility to biomolecules delivered in the microfluidic devices, the charged interface described could provide a promising option.