In well logging area, along with the widely application and advancement of NMR technology, new pulse sequences have been proposed successively, which inspires more complicated demand for the pulse programmer of NMR well logging tools. In this context, the new pulse programmer must fulfill the requirements including high accuracy, flexible programmability and well generality. In order to meet the latest as well the traditional demand, based on the summary of the features of traditional pulse sequences and new pulse sequences, this paper proposes the logic design which can derive pulse sequences as desired by configuration. The key design specification is illustrated. Then it is verified by programmable logic device FPGA. This pulse programmer can generate CPMG, DE pulse sequence and other terms of pulse sequences, which performs well flexibility and universality.