It is a challenge to determine selenium in acid aqueous for environmental monitoring and selenium-rich agricultural diagnosis. Herein, we developed a novel localized surface plasmon resonance (LSPR) sensor to detect Se(IV) ions based on the extraordinary laterals etching of gold nanorods (AuNRs). The etching started from the laterals in the low amount of Se(IV) ions, and accompanied by an apparent red shift of the longitudinal plasmon band (LPB), and then transformed to the tips etching with the upward of Se(IV) ions, the LPB band immediately shifted to the shorter wavelength. The red shift change (Δλ) of LPB band was utilized to quantitative analysis instead of blue shift or absorbance intensity, which gave a high selectivity for the proposed sensor. More importantly, this sensor could be performed in 0.1 mol/L of HCl solution, which achieved the seamlessly jointing with the pretreatment of complex samples, without time-consuming pH adjustment.Successful selenium detection was demonstrated in complex soybean samples that collected from the maturity after spraying organic chelated selenium at full flower period. The sensor provided a promising way to monitor and diagnose selenium in complex environmental samples and selenium-rich crops.