The inherent content of calcium in milk powder was rapidly determined by using the nonlinear chemical fingerprint method. Firstly, the inherent calcium content in three brands of milk powder was determined by using flame atomic absorption spectrometry as described by GB 5413.21—2010 (National Standards of PR China). Different contents of calcium carbonate were added into the above three brands of milk powder, respectively. Using“H+Mn2++BrO-3+acetone+substrates in milk powder” as reaction system, the nonlinear chemical fingerprints of milk powder with different calcium contents were obtained, and there was a linear relationship between the undulatory period and the total content of calcium in milk powder, where the total content of calcium consisted of the inherent calcium content in milk powder and the calcium content of being added into milk powder. Then, the inherent content of calcium in milk powder was calculated by using the least square method. The results showed that the total content of calcium in milk powder and the undulatory period value had a good linear relationship within 0.0227～0.0323g range of the total content of calcium when the total amount of milk powder was 0.9g, the determination coefficient was 0.9953～0.9988, the recovery rate was 99.18%～101.60%, the RSD was 0.47%～1.63%, and the determination range of the inherent calcium content in milk powder was 0～0.0323g. The method developed has advantages of good accuracy and simple operation, and it is a practical and feasible method for determining the inherent calcium content in milk powder. In addition, the method can be used for reference in research on the methods for the determination of other components in other complex samples.