Multi-sublattice antiferromagnets with complex crystallographic structures can give rise to non-trivial spin ordering due to competing exchange couplings within and between different subsystems of magnetic ions. In nickel orthoborate Ni3(BO3)2 there are two distinct subsystems of the Ni2+ ions (S = 1) that are antiferromagnetically ordered below TN = 46 K, forming complex spin ordering and multiple branches of magnons. We report a comprehensive experimental study of single-crystal spin dynamics using polarized Raman scattering and infrared absorption spectroscopy. A rich multi-branch spin-wave spectrum covering a broad energy range was observed via one-magnon scattering. Additionally, we detected the formation of a complex-shape two-magnon band in the range of 60–200 cm−1. These findings were supported by calculations using linear spin-wave theory, which allowed us to describe the shape of the two-magnon band and propose an exchange structure for the antiferromagnetic nickel orthoborate Ni3(BO3)2 compatible with experimental observations.