Ammonium polyphosphate (APP) was prepared by the co-rotating twin-screw extrusion of monoammonium phosphate (MAP) and urea for potential application as a slow-release fertilizer. A fundamental study to establish a possible polycondensation mechanism was carried out using thermal analysises and the screw pullout technique. A two-step mechanism, MAP polycondensation and pyrophosphate polycondensation, was verified. Furthermore, a urea-phosphate intermediate was identified by X-ray photoelectron spectroscopy (XPS), allowing us to break the system down into basic reactions. To support the mechanism, a kinetics model of the overall conversion reaction was established based on ion chromatography (IC) data. The inactivation effect of the intermediate polyphosphate was found to increase the polydispersity index (PDI, defined as the ratio of the weight-average molecular weight to the number-average molecular weight, Mw/Mn) of APP. The resulting multiformity led to an optimized phosphorus release curve over the crop growth cycle. This work adds to earlier studies on APP synthesis, allowing synthetic control at the molecular weight distribution (MWD) level rather than the general polymerization level.