Composition changes of swine manure and the effects on MAP ($MgNH_4PO_46H_2O$) crystallization by microwave irradiation were examined. The concentration of ${PO_4}^{3-}$ was increased within a fixed period of time and then decreased, but $NH_4$-N was reduced continuously during microwave irradiation. Concentration of ${PO_4}^{3-}$ was started to reduce just from the point of foam formation during microwave irradiation, and the temperature at that time was always $49^{circ}C$ irrespectively to microwave irradiation rate. Inorganic carbon was reduced with microwave irradiation, but soluble organic carbon (TOCs) was increased proportionally. Crystallization rate under conditions of non-microwave irradiation, irradiation up to $93^{circ}C$ and $48^{circ}C$ was 87.8%, 87.3% and 98.5%, respectively, showing 10% enhancement when irradiated up to $48^{circ}C$. However, removal efficiency of ammonia nitrogen was proportional to the microwave irradiation rate or duration, obtaining 2.5%, 4.5% and 10.2%, respectively. Based on these results, it would be a useful strategy to irradiate microwave up to $49^{circ}C$ to enhance MAP crystallization rate by changing the ionic pattern of nutrients in the manure. Meanwhile, provision of enough microwave irradiation rate might be needed to achieve high $NH_4$-N removal.