Hydroxymethyl phosphonates (HPs) are important organic chemical raw materials and intermediates. HPs are generally synthesized by phosphite esters and formaldehyde using the conventional organic synthesis device. It shows the disadvantages of strong heat-release and more by-products for the reaction, and high acid number (AN), low yield and low purity for the product. We have designed a microfluidic reactor to synthesize HPs that can overcome above mentioned disadvantages. During the microfluidic reaction process, a series of reaction conditions can be controlled precisely. According to adopt the optimal reaction conditions, five HPs were obtained with low AN (<0.15 mg KOH/g), high yield (>94%) and high purity (>99%). The designed microfluidic reactor can reduce labor cost, save equipment area, and cut down the amount of wastewater. The synthesis process can also realize continuous production and scale-up production with no amplification effect.