We calculate the PCAC mass for $(2+1)$ flavor full QCD with Wilson-type quarks. We adopt the Small Flow-time eXpansion (SFtX) method based on the gradient flow which provides us a general way to compute correctly renormalized observables even if the relevant symmetries for the observable are broken explicitly due to the lattice regularization, such as the Poinc{a}re and chiral symmetries. Our calculation is performed on heavy $u, d$ quarks mass ($m_{pi}/m_{rho}simeq0.63$) and approximately physical $s$ quark mass with fine lattice $a simeq 0.07$~fm. The results are compared with those computed with the Schrodinger functional method.