Accurate identification and quantification of methamphetamine (MA) and its related substances are essential for the investigation and fair trial of drug offenses. In this study, a modified LC-ESI-MS/MS method for the simultaneous determination of MA and its isomer N-isopropylbenzylamine (N-IBA) in forensic samples was developed and validated. Optimum chromatographic separation of the target analytes was achieved on an Agilent Poroshell 120 SB-C18 column ( 4.6 × 100  mm, 2.7 μm) at 40°C with isocratic elution at the flow rate of 0.40 mL/min. The mobile phase was acetonitrile and 20 mM ammonium acetate solution containing 0.1% formic acid (80 : 20, v / v ). Positive ESI-MS/MS detection was performed in multiple reaction monitoring (MRM) mode to identify and quantify the target analytes. Method validation showed excellent linearity in the range of 0.51 ng/mL~51 ng/mL for MA and N-IBA. The low limit of detection (LLOD) and low limit of quantification (LLOQ) reached 0.1 ng/mL and 0.3 ng/mL for both analytes. The method showed a satisfactory accuracy with an inter- and intraday-relative error (RE) <20%, and a precision of inter- and intraday relative standard deviation (RSD) less than 15%. The validated method was successfully applied in real forensic samples and resulted in the detection of MA and N-IBA in 8 suspected samples in drug cases that only deemed MA positive using our previous routine screening procedure, which avoided the misidentification of N-IBA as MA.