High-purity FePO4 with small particle size is pivotal for improving electrochemical performance of LiFePO4-based lithium-ion batteries. Here, an oscillating feedback microreactor (OFM) based on chaotic advection was designed to prepare high-quality FePO4 by coprecipitation. Dye-tracer experiments and CFD simulations were adopted to investigate fluid mixing mechanism and to evaluate mixing efficiency in the reactor. The results indicated that a “flow-focused” OFM (FOFM) performed better than a “Y-junction” OFM in mixing performance, owing to enhanced premixing in focused inlet microchannel of the former. The results of Villermaux-Dushman experiments illustrated that almost complete mixing could be achieved in 0.16 ms in FOFM. Accordingly, FePO4 nanoparticles of good quality was synthesized using FOFM, and the particle size can be easily controlled by adjusting flow rate or reactant concentration. High-purity (P/Fe molar ratio: 0.95–1.04) and ultra-small FePO4 nanoparticles (9 nm) with narrow particle size distribution were generated at a high throughput of 180 mL/min.