Porous graphene, which features nano-scaled pores on the sheets, is mostly investigated by computational studies. The pores on the graphene sheets may contribute to the improved mass transfer and may show potential applications in many fields. To date, the preparation of porous graphene includes chemical bottom-up approach via the aryl-aryl coupling reaction and physical preparation by high-energy techniques, and is generally conducted on substrates with limited yields. Here we show a general and scalable synthesis method for porous graphene that is developed through the carbothermal reaction between graphene and metal oxide nanoparticles produced from oxometalates or polyoxometalates. The pore formation process is observed in situ with the assistance of an electron beam. Pore engineering on graphene is conducted by controlling the pore size and/or the nitrogen doping on the porous graphene sheets by varying the amount of the oxometalates or polyoxometalates, or using ammonium-containing oxometalates or polyoxometalates.