A mode-locked radially polarized laser is generated based on the difference of thermal focal length in side-pumped Nd:YAG and the condition of mode-locking by the semiconductor saturable absorption mirror (SESAM). The spot size of radial polarization and azimuthal polarization with different pumping currents, and the parameters of the LD side-pumped Nd:YAG four-mirror-folded passively mode-locked cavity are analyzed. The maximum output power of 13 W with the frequency of 59 MHz and the wavelength of 1064 nm is acquired. We demonstrate that the purity of the radially polarized beam is more than 92%.