This paper proposes an approach to derive the Jacobian matrix of a hybrid mechanism by applying a velocity operator to the transformation matrix. This Jacobian matrix is capable of deducing hybrid singularities, which cannot be identified by using the screw-based Jacobian or velocity-based Jacobian. The transformation matrix was obtained based on the algebraic geometry approach, and it becomes the key point since it was used to not only formulate the Jacobian matrix, but also to define the motion type of hybrid mechanisms. In this paper, two hybrid mechanisms were investigated, which were composed of two distinct parallel mechanisms mounted in series. Hybrid Mechanisms 1 and 2 were composed of 3-PRP-3-RPS and 3-RPS-3-PRP (the underlined P is an actuated joint), respectively. The motion types of Hybrid Mechanisms 1 and 2 were determined from the product of the transformation matrices of the 3-PRP and 3-RPS parallel mechanisms, and vice versa. The developed method was employed to establish the Jacobian matrix to which the conditioning index was applied. Therefore, the kinematic performances of the two hybrid mechanisms can be compared for a given bone surgery trajectory within the workspace. It turns out that Hybrid Mechanism 1 has superior performance than that of Mechanism 2, which indicates that Mechanism 1 is better at transmitting power to the moving platform.