Display omitted •The N-doped TiO2 microspheres and Si/N-TiO2 nanocrystals were synthesized through the one-step hydrolysis method.•The cross-linking state between nanocrystals increases the oxygen vacancy concentration and provides more transport channels.•The positively charged nanocrystals had a repulsive effect on the cationic pollutants.•Removal efficiency of 1.0 g L−1 Cr(VI) in 120 min was as high as 53%. This paper focuses on a novel one-step co-hydrolysis synthesis strategy of silicon modified N-doped titanium dioxide nanocrystals and its application in the visible light photocatalysis of chromium at g L−1 level in wastewater. Titanium(IV) bis(ammonium lactato)dihydroxide (TALH) has been adopted firstly as both Ti and N sources for synthesis of N-doped TiO2 microspheres (N-TiO2). Si modified N-TiO2 was fabricated by adding γ-(2,3-epoxypropoxy) propyltrimethoxysilane (KH560) before hydrolysis of TALH. The adsorption and co-hydrolysis of silane molecules significantly inhibit the growth of N-TiO2 crystals, and further promote appropriate cross-linking of particles through silanol (hydrolysate) intermolecular force or potential Si-O-Si bond by the polycondensation reaction to form nano-sized Si/N-TiO2. Interestingly, the introduction of silicon turns the negative charge surface of N-TiO2 into positive charge one through the Si-O-N-Ti/Si-N-O-Ti bond, and improves the adsorption of Cr(VI). Systematic characterization and photocatalytic test documented that abundant adsorption pores, large amount of oxygen vacancies and transport channels jointly accelerate the reduction of Cr(VI) on Si/N-TiO2 nanocrystals surface. Up to 98.7% (30 min for 0.2 g L−1) and 53.2% (120 min for 1.0 g L−1) removal efficiency, importantly, confirmed that the Si/N-TiO2 nanocrystals was competitive for the treatment of highly Cr(VI) containing wastewater.