Depolarization mechanism and compensation scheme of radially polarized beams under non-uniform pumping were investigated. Theoretical analysis shows that, for the non-uniform pumping status, the thermal induced shear birefringence caused by the thermally induced shear stress within the cross-section of the isotropic crystal is the main reason for the depolarization of the radially polarized beams. Related experiments were designed to evaluate the depolarization of the radially polarized beams under non-uniform pumping conditions by using two methods of thin-film polarizer (TFP) measurement and purity measurement, in which the TFP measurement method was used to detect the overall depolarization of radially polarized beams and the purity measurement method was used to detect local depolarization of radially polarized beams. With a peak pump power of 1.1 kW, the depolarization measured by the two evaluation methods was 2.34% and 2.53%, respectively. Based on the theoretical analysis and evaluation results, a combination of phase modulation and spatial mode matching was considered in the design of the depolarization compensation scheme, which improved the depolarization of the radially polarized beams by 59%. Meanwhile, a picosecond radially polarized beam with a pulse energy of 19.36 mJ, a purity of 90.13%, and a beam quality M² factor of 3.8 was achieved.