Characterizing the fidelities of quantum gates and improving them are essential requirements to build a scalable quantum computation platform. Two typical methods for such purpose, i.e., randomized benchmarking and quantum process tomography, contain drawbacks that cannot be compensated without the aid of the other, which demands the development of a new stand-alone protocol. Gate set tomography (GST) is one of such protocols developed to obtain detailed information of qubit gates that are free from the state preparation and measurement (SPAM) errors. We have implemented GST on single transmon qubit embedded in a three dimensional cavity. As a result, GST analysis not only estimated the process matrices of target gates but also suggested the direction for further calibration to achieve more accurate gate operations.