Disclosed are a cutting method of flexible display panel, a controlling device in the cutting method and a cutting apparatus of flexible display panel. The cutting method comprises steps of placing a transparent substrate (21) carried with a flexible film layer (22) on a base (10); cutting only the transparent substrate (21) by means of a cutting tool (30); obtaining a cutting trace of the cutting tool (30); and controlling a laser knife (40) to cut the flexible film layer (22) carried on the transparent substrate (21) along the cutting trace of the cutting tool cutting the transparent substrate. In this way, by controlling the laser knife (40) to cut the flexible film layer (22) disposed on the transparent substrate (21) following the cutting trace of the cutting tool (30) cutting the transparent substrate (21), the flexible film layer (22) can be completely cut at the same time when or after the transparent substrate (21) is completely cut, so as to avoid rough selvedges during cutting the flexible film layer (22), thereby improving the cutting effect of cutting the flexible display panel; besides, in case that the cutting tool (30) and the laser knife (40) operate in parallel cutting mode, it can also improve the cutting efficiency.