With the isovector coupling constants adjusted to reproduce the physical pion mass and lattice QCD results in baryon-free quark matter, we have carried out rigourous calculations for the pion condensate in the three-flavor Nambu-Jona-Lasinio model, and studied the three-dimensional QCD phase diagram. With the increasing isospin chemical potential , we have observed two nonzero solutions of the pion condensate at finite baryon chemical potentials , representing, respectively, the pion superfluid phase and the Sarma phase, and their appearance and disappearance correspond to a second-order (first-order) phase transition at higher (lower) temperatures and lower (higher) . Calculations by assuming equal constituent mass of and quarks would lead to large errors of the QCD phase diagram within , and affect the position of the critical end point.