Structured illumination (SI) involves projecting controlled spatial light patterns onto a scene or sample and processing the captured response to recover information such as the phase, surface shape, or optical contrast. Three-Step Phase Shifting (TPS), also known as three-phase demodulation (TPD) in the spatial frequency domain imaging (SFDI) field, is a common SI workflow in which three phase-shifted sinusoidal patterns are projected and captured sequentially for one demodulation. To achieve acceptable demodulation quality, all three phase-shifted patterns must be captured correctly. However, achieving this quality introduces a trade-off since each phase must be captured at the correct time, increasing acquisition time and requiring precise projector–camera synchronization. In real-time TPD-based SI, low pattern-generation throughput, synchronization uncertainty, and often bulky desktop implementations remain major limitations. Therefore, this work investigates, designs, and validates a deterministic, low-latency, and portable projection–capture synchronization system for TPD-based SI. First, a Hyperspectral (HS) Python-based SI (HSPy-SI) system, representative of common state-of-the-art (SOTA) implementations, is evaluated. It uses an HS snapshot camera and a fixed-delay desktop synchronizer. Then, the proposed HyperSI system is introduced as a real-time projection–capture synchronizer implemented as a bench-top prototype on heterogeneous embedded platforms: a Single-Board Computer (SBC) and a System-on-Chip (SoC) board. Its core contribution is a tunable parameter, W (Frame Count to Wait), which counts frame-generation interrupts before capture and reduces the delay-search space. Compared with the SOTA, HyperSI achieves over 8× higher pattern-generation throughput, increases polarized acquisition by 7× to nearly 4 FPS, reaches about 12 FPS without polarizers, and reduces waiting time by 88×.