Inositol phosphates (InsPs) have important biological functions and multiple nutritional effects. Breeding and nutrition studies of InsPs require a simple, rapid, and accurate method for high-throughput quantification. Here, we developed an ion-pair chromatography/tandem mass spectrometry (IPC/ESI–MS/MS) method for the simultaneous separation and determination of each InsP. A highly volatile ion-pair reagent (dihexylammonium acetate, DHAA) was applied to separate InsP1–InsP6, which were then quantified by multiple reaction monitoring (MRM) in negative ESI mode. This method could simultaneously detect InsP1–InsP6 within 15 min and exhibited a wide linearity (typically 0.3–1200 pmol). The lower limit of detection was 0.3 pmol for all InsPs, excluding InsP2 (0.15 pmol) and InsP6 (3 pmol). The method accuracy of all analytes ranged between 87 and 111% with the inter- and intra-day precision of 0.9–15 and 2.2–11%, respectively. This method was successfully applied to quantitate InsPs in different types of crop seeds, organs, and a maize inbred germplasm collection composed of hundreds of inbred lines, showing its potential for promoting the nutrition and genetic research of InsPs.