The quantum gate, as the foundation of quantum computation, depends on the architecture of the quantum chip, especially in superconducting systems. The parametric modulation to the flux bias is an important protocol to realize the multi‐qubit gate, which has some intrinsic advantages. Similar to other two‐qubit operations, parametric gates leave the extra phase in single‐qubit space, which is required to be corrected. In this article, the relation between the phases of the modulated pulse and the applied microwaves is experimentally characterized. By adjusting the envelope shape and phase of the applied pulses, the extra phase of the one qubit generated by the two‐qubit gate is suppressed via a simple and fast Ramsey‐like experiment. The tomography results demonstrate that this protocol is an effective calibrating method for future large‐scale quantum circuit manipulation.