This paper presents balance and vibration control algorithm for bipedal humanoid robots in the motion embedded CoM Jacobian framework. The vibration control is employed during a single supporting phase, which can suppress residual vibration of the un-modelled flexibility. Because the previously proposed walking control method in the resolved momentum control framework is based on the rigid body motion, vibration control algorithm which compensates for residual vibration can make the humanoid motion into rigid body motion. The vibration control consists of the modified global planning CoM trajectory and modified ankle joint controller in the motion embedded CoM Jacobian framework. The parameters of the controller are acquired easily using MATLAB System Identification Tool box. Also, balance control algorithm which controls body orientation is applied to the whole body coordination framework. By dynamic walking experiments using a humanoid robot MAHRU-R, the validity of the proposed control methods is verified.