A novel design of Composite Turbo-Molecular Pump (CTMP) is proposed. The major configuration of CTMP is composed by a coarse pump, a Turbo-Molecular Pump (TMP) and a Magnetic Gear Unit (MGU) capable of speed amplification. The corresponding modal analysis and the study on rotor/bearing dynamics are undertaken at first to estimate the resonance frequencies of the TMP blade rotor itself solely and the interactive dynamics of Blade Rotor/Radial Active Magnetic Bearing (BR/RAMB) subsystem. Secondly, an appropriate interval of stiffness provided and tuned by the RAMB is presented to make the TMP blade rotor able to actively retain speed margin at least 10% away from the resonance frequencies of the closed-loop control system. Thirdly, an economical and efficient method by adjusting the angular acceleration speed of BR, namely Resonance-Driven Prevention Strategy (RDPS), is proposed to avoid the undesired excitation at resonance frequencies of BR/RAMB system and potential instability. Finally, by intensive computer simulations, the proposed RDPS indeed manifests its outstanding performance to efficiently skip or bypass the natural frequencies of the closed-loop system within a very short time period and guarantee, to a certain extent, the system stability.