Abstract Magnetic reconnection preferentially takes place at the intersection of two separatrices or two quasi-separatrix layers, which can be quantified by the squashing factor Q, whose calculation is computationally expensive due to the need to trace as many field lines as possible. We developed a method (FastQSL) optimized for obtaining Q and the twist number in a 3D data cube. FastQSL utilizes the hardware acceleration of the graphics processing unit and adopts a step-size adaptive scheme for the most computationally intensive part: tracing magnetic field lines. As a result, it achieves a computational efficiency of 4.53 million Q values per second. FastQSL is open source, and user-friendly for data import, export, and visualization.