We have explored the skyrmion phases and phase diagram of poly- and single-crystal MnSi by the measurements of the magnetoelectric coefficient αE and ac magnetic susceptibility of the MnSi/0.7Pb(Mg1/3Nb2/3)O3–0.3PbTiO3 composite. We found that the regular skyrmion lattice phase in the single-crystal sample has been averaged in the MnSi polycrystal due to random grain orientations, which results in an extended skyrmion lattice-conical mixture phase down to 25 K. The magnitude of the out-of-phase component in αE of the polycrystal, not single crystal, decreases gradually with decreasing frequency. With the changing of the driven ac field, we reveal a depinning threshold behavior in both samples. The depinning field is stronger in the polycrystal than that in the single crystal and may be responsible for the diminishing of the dissipative behavior at lower frequency due to grain boundaries and defects. The composite magnetoelectric method provides a unique approach to probe topological phase dynamics.