By controlling the SPS temperature, we prepared Zintl Zr3Ni2.9Co0.1Sb4 samples, namely Co doping in Ni sites of Zr3Ni3Sb4, and investigated the corresponding thermoelectric properties. It was found that a significant reduction of the lattice thermal conductivity occurred due to Co-doping while tuning the SPS temperature slightly affected ZT values. The influence of aliovalent element Co doping on the phonon structure and transport properties of Zr3Ni3Sb4 was conducted through first-principles calculations. Co-doping enhanced phonon anharmonicity and induced a completely avoided crossing between acoustic and optical phonons, which resulted in the suppressed phonon velocity and lifetime, leading to a remarkable reduction in lattice thermal conductivity. Our finding enriches the understanding of aliovalent doping in thermal transport theories which should be applicable to other thermoelectric systems.