The paper presents a new method to remove baseline drift in the brain blood stream signal based on cubic spline interpolation theory. Firstly, detect some characteristic points in the original signal, and then fit the drifting baseline based on the cubic spline interpolation technique. Finally the original signal minus the baseline is the steady signal of brain blood stream. Lots of simulation experiments and clinical tests had been done, and the baseline drift in LabVIEW software program was removed perfectly. Once the method to remove baseline drift is put in practice, its effect is good and its speed is fast, and it is easy to carry out. It has great application in brain wave monitor with embedded CPU and real time character, and it is also applied in other signal detectors.