A chromatographic analysis method for determining inorganic anions and melamine in fertilizers was established using ion chromatography (IC). The fertilizer samples were extracted by ultrasonic method with 7 g/L trichloroacetic acid solution and centrifuged. The supernatant is purified by a solid phase extraction column. Then, the anions in the solution were purified using SH-AP-1 (250 mm×4.0 mm) as a separation column, and measured by a suppressed conductivity detector; the melamine in the solution was separated using SH-CC-4 (200 mm×4.0 mm) as a separation column and detected by a UV detector. The results show that the mass concentration of anions had a linear relationship with its peak area within a certain range, the linear correlation coefficient r of the standard curve was greater than 0.999, the recovery rate of spiked samples was 93.4%-104.4%, and the relative standard deviation (RSD) of the measured value (n = 6) was less than 4%. Thus, this method is widely suitable for detection of anions and cations in a variety of fertilizer samples.