As a new multifunctional material, strontium titanate (SrTiO3) ceramic has a wide application in grain boundary layer capacitor (GBLC) with the microstructure characteristics of semi-conductive crystalline grain and insulated boundary. An ultra-precision nanofishing technique is developed to lap and polish the brittle and thin SrTiO3 substrate with the cluster MR-effect plate where the abrasives are constrained by the cluster MR-effect chains, under the influence of a magnetic field, the carbonyl iron particles (CIPs) and non-magnetic abrasive particles remove material from the surface of workpiece being machined in this paper. Mahr XT20 roughmeter, Keyence VHX-600 and Olympus S4000 microscopes are used to investigate the characteristic of machined surface and the mechanism of material removal. An ultra-smooth planarization surface of SrTiO3 substrate with surface roughness Ra 3.8 nm (Mahr), RMS 0.973 nm (Veeco interferometer) is obtained under a high efficiency. It is found that the pore structures of the sintered substrate would weak the machinability of SrTiO3 and influence the further improvement of surface quality.