Conventional nuclear magnetic resonance (NMR) instruments are large and difficult to carry, which limits their application in fields such as on-site petroleum exploration, food safety, environmental pollution, and quality control. To address this issue, this paper proposes a design of a handheld NMR console. By utilizing an advanced RISC machine (ARM) core construction, field programmable gate array (FPGA) logic design and control program design on a programmable system-on-chip Zynq-7000, the entire handheld NMR console was designed and implemented. After completing the entire design, several basic pulse sequences, including free induction decay (FID), spin echo (SE), and Carr-Purcel1-Meiboom-Gill (CPMG), were tested on a 0.5 T desktop NMR system developed by our research group. The tests validated the correctness of the overall architecture design and the coordination among various modules. The designed NMR console is 10.6 cm long, 6.0 cm wide, and 1.9 cm high, which significantly reduces the size while enhancing the real-time performance of pulse sequence and improving the stability of the console, laying a foundation for further development of portable NMR instruments.