The generation of combinatorial oligonucleotide libraries is desirable for applications such as DNA aptamers, data storage, DNA origami, or synthetic genomes, but conventional libraries present challenges in detection and analysis. Synthesis of unique oligonucleotide sequences on magnetic nanoparticles would enhance the ability to manipulate, recover, and detect them. Here, we present a protocol for generating a scalable combinatorial oligonucleotide library on magnetic nanoparticles using split-and-pool synthesis. We then describe the process for preparing the library for conventional and next-generation sequencing (NGS) DNA sequencing. For complete details on the use and execution of this protocol, please refer to Nguyen et al.(1).