We report a comparative study of the critical current density (Jc) and vortex pinning among pure and Mn doped KxFe2−ySe2 single crystals. It is found that the Jc values can be greatly improved by Mn doping and post-quenching treatment when comparing to pristine pure sample. In contrast to pure samples, an anomalous second magnetization peak (SMP) effect is observed in both 1% and 2% Mn doped samples at T = 3 K for H∥ab but not for H∥c. Referring to Dew-Hughes and Kramer's model, we performed scaling analyses of the vortex pinning force density vs magnetic field in 1% Mn doped and quenched pristine crystals. The results show that the normal point defects are the dominant pinning sources, which probably originate from the variations of intercalated K atoms. We propose that the large nonsuperconducting K-Mn-Se inclusions may contribute to the partial normal surface pinning and give rise to the anomalous SMP effect for H∥ab in Mn doped crystals. These results may facilitate further understanding of the superconductivity and vortex pinning in intercalated iron-selenides superconductors.