Co-Pd alloy thin films prepared by a DC-sputter that have self-organized nano structure(SONS), are promising for high-density information storage media in information era. We prepared the samples by varying Pd contents of 0~8.1 wt% at the substrate temperatures of room temperature (RT) and 200 $^{circ}C$, respectively Microstructure and Pd contents of the Co$_{1-x}$ Pd$_{x}$ films are probed by a scanning electron microscope (SEM), a transmission electron microscope (TEM) and an energy dispersive spectrometer (EDS). We also investigated the saturation magnetization (Ms), remanence and coercivity of the Co$_{1-x}$ Pd$_{x}$ films. Surface roughness are measured by an atomic force microscope (AFM). We revealed that self-organized nano size Co-enriched phase and Pd-enriched phase existed with Pd contents at the substrate temperatures of RT and 20$0^{circ}C$ through microstructure characterization. SONS helped to keep the saturation magnetization and enhance the perpendicular anisotropy with Pd contents. Out result implies that we may tune the perpendicular magnetic properties with keeping the saturation magnetization by varying substrate temperatures and Pd contents for high density magnetic recording.rding.