Nuclear spin singlet state is a special spin state, whose main characteristic is that its lift-time can be much longer than the corresponding longitudinal/transverse relaxation time. It can be used to study molecular slow diffusion, slow motion, special signal selection or other molecular motion. In the literature, singlet states are mainly studied in an isolated two-spin system. Here we discuss the nuclear spin singlet state preparation in a three-spin system. The system consisting of three protons in the molecule N-acetyl aspartic acid (NAA) was used as an example. Specifically, we used optimal control theory and numerical calculation method to design the pulse sequence and to transfer the two spins in methylene group into singlet state. The shaped pulses including and not including the proton in the methyne group were designed respectively. Our simulation results indicate that to ensure a high efficiency for the singlet state preparation, the coupling of the proton in the methyne group should be included in the pulse calculation. Furthermore, the singlet state can be combined with two-dimensional pulse sequences such as COSY and NOESY. The experimental results show that some correlation peaks could be selectively observed in the two-dimensional spectrum based on singlet state. It will be useful for the spectral peak assignment especially in the case of serious spectral overlap.