Dynamical decoupling is widely used in many quantum computing systems to combat decoherence. In a practical superconducting quantum system, imperfections can plague decoupling performance. In this work, imperfections in a superconducting qubit and its control system are modeled via modified Hamiltonian and collapse operator. A master equation simulation is carried out on the qubit under 1/f environment noise spectrum. The average dephasing rate of qubit is extracted to characterize the impact of different imperfections on the decoupling from dephasing. We find that the precision of pulse position, on–off ratio, and filtering effect are most critical. Bounded pulses have weaker impact, while variation in pulse width and qubit relaxation are insignificant. Consequently, alteative decoupling protocols, jitter mitigation, cascaded mixers, and pulse shaping can be conducive to the performance of decoupling. This work may assist the analysis and optimization of dynamical decoupling on noisy superconducting quantum systems.