This paper describes and establishes a new method that examines the sequence of two crossing strokes in different colors in a questioned document. In order to identify the writing sequence, an empirical method is usually used to find out some physical evidence by human eyes with a microscope. However, owing to the phenomenon of mixed inks in the intersection, there is still some drawbacks with the conventional approaches. Hence, in addition to the empirical method, a new method using Laser Scanning Confocal Microscope (LSCM) is adopted. Unlike the conventional light source, the LSCM system uses a krypton argon laser source to emit a laser beam of three different wavelengths. The beam goes through a scanning control unit to act as the function of light scanning, and passes through the objective lens of microscope to the surface of crossing strokes. Reflected light goes the same pathway back to the scanning control unit and is collected by a photomultiplier where the image is reconstructed from a series of signals derived from the photomultiplier output, and saved onto a personal computer. It is necessary to scan the point probe over the field of view and capture sectional images in various depths. By overlaping every sectional image followed by computerized reconstruction, we can observe the evidence to help identify the writing sequence in the questioned document by means of a stereo spectacles. Experimental results show that with the help of the LSCM, together with the method we developed, more accurate judgments are achieved.