2,4-Dinitroanisole (DNAN) is being used as a replacement for 2,4,6-trinitrotoluene (TNT) as a less-sensitive melt-cast medium explosive than TNT. In this paper, we studied the surface-enhanced Raman spectroscopy (SERS) analysis of DNAN using Ag nanoparticles (AgNPs) modified by L-cysteine methyl ester hydrochloride. Due to the formation of a Meisenheimer complex between DNAN and the modifier, the modified AgNPs can detect 20 mu g/L (0.2 ng) and 0.1 mg/L (1 ng) DNAN in deionized water and aged tap water, respectively. Three other chemicals (L-cysteine, N-acetyl-L-cysteine, and L-cysteine ethyl ester hydrochloride) were used as AgNPs modifiers to study the mechanism of the SERS of DNAN. It was confirmed that the amino group of L-cysteine methyl ester hydrochloride was the active group and that the methyl ester group significantly contributed to the high SEAS sensitivity of DNAN. In order to further test the mechanism of Meisenheimer complex formation, the effect of anions and cations present in natural water on the SEAS of DNAN was studied. It was found that CO(3)(2-), Cl(-), and K(+) at 100 mg/L did not negatively affect the SEAS of 10 mg/L DNAN, while SO(4)(2-), Na(+), Mg(2+), and Ca(2+) at 100 mg/L significantly quenched the SERS of 10 mg/L DNAN. The negative effect of the bivalent cations could be offset by SO(4)(2-).