Electronic-grade ammonia plays a critical role in semi-conductor manufacturing, where its purity directly impacts the performance of semiconductor devices and process yield. To ensure trace anions (such as Cl−, NO3−, and SO42−) in electronic grade ammonia are controlled at ultra-low concentration levels, an analytical method based on two-dimensional ion chromatography (2D-IC) and online neutralization valve switching technology has been developed. The proposed technique enables simultaneous quantification of eight key trace anions in ammonia, employing precise valve switching and optimized neutralization suppression to overcome interference from high-concentration alkaline matrices. Through online secondary neutralization and optimized configuration of anion enrichment columns, the experimental setup successfully eliminated matrix effects from the alkaline medium, significantly enhancing analytical sensitivity and selectivity. The optimized method achieved trace anion detection at the μg/kg level, with validation experiments demonstrating high accuracy and reproducibility. Furthermore, recovery rates ranged from 81.1 to 107.3%, and precision for all target anions at different spiked concentrations remained below 3%. This method complies with SEMI standard requirements and provides a reliable analytical approach for quality control of electronic grade ammonia.