It is convenient to calculate derivative in wave number space using the inbuilt FFT function in Matlab. This paper describes a matlab algorithm for derivative calculation of 1D gravity and magnetic anomaly in wave number space, gives code of program and deals with some programming skills for precision improvement. Through model test and data analysis, it is found that the precision of the FFT method is much higher than that of the Fourier Series method in vertical derivative calculation. In horizontal derivative calculation, however, the precisions of the two methods are almost the same. During kainite exploration in a certain basin, satisfactory result was obtained in the processing of gravity profile data using this method.