Proton decay matrix elements in QCD are indispensable quantities to constrain GUT models through the lower bound of the proton lifetime measured in the current and future underground experiments. Results obtained with lattice QCD so far have potentially largest systematic uncertainty on the chiral extrapolation. We report on the relevant form factors of one of the dominant decay processes: a proton decaying into a pion and an anti-lepton with a three-quark operator, using the physical-point, improved Wilson-fermion configurations generated by the PACS collaboration at the lattice spacing of 0.084fm.