The invention relates to a cut stem quality control method and system based on cut stem drying. The method includes the steps of determining a variation region of an outlet water difference value by selecting outlet water as a factor for influencing the cut stem drying quality and counting the difference between the outlet water and a target value, dividing the outlet water into N sections according to the size of the difference between the outlet water and the target value, collecting current outlet water, conducting section judging according to the difference between the currently-collected outlet water and the target value, and adjusting the opening degree of a hot air door of the second section according to the variation of the sections so as to achieve the control over the sections of the outlet water. The quality characteristic index of an original cut stem making procedure can be greatly improved, the abnormal interference overcoming and eliminating capacity in the cut stem drying process is enhanced, process capability is improved, the outlet water in cut stem drying and the stability of the outlet water are sufficiently ensured, complete automatic control is achieved, labor intensity is relieved, and product quality is improved.