The spin-polarized scanning tunneling microscope (SP-STM) has been employed to enhance its capabilities of detecting the electronic and magnetic properties of organometallic molecules. Using a tip functionalized with a cobaltocene (Cc) molecule, recent SP-STM experiment performed on the Cu-tip/Cc/Fe/Cu(100) composite junction revealed an asymmetric Kondo resonance splitting in the differential conductance (dI/dV) spectrum. However, a systematic theoretical simulation of such system is lacking, and the important roles of the substrate spin-polarization and the Fe adatom still remain to be elucidated. In this work, by combining density functional theory and the hierarchical equations of motion methods, we achieve first-principles-based simulations of the tip control process of the Cu-tip/Cc/Fe/Cu(100) junction. We correctly reproduce the experimental results and demonstrate the influences of the Fe adatom on the spin-polarization of the substrate and on the Kondo resonance splitting in the dI/dV spectra.