Algal toxin analysis, particularly for microcystin (MC) variants, is commonly performed using LC-MS/MS as the standard method. In 2016, the environmental protection agency (EPA) published method 546 for the determination of total MCs by ELISA. However, the limited availability of commercial algal toxin standards limits the efficacy of the LC-MS/MS method. This study proposes a novel approach using the 2-methyl-3-methoxy-4-phenylbutyric acid (MMPB) structure generated by oxidizing MCs with potassium permanganate and sodium periodate. MMPB is formed through the oxidation of the common (all-S,all-E)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid (ADDA) structure, eliminating the need for specific standard materials for each MC variant. This provides a method for measuring the total MCs. This study focused on optimizing sample pretreatment before oxidation, salt removal as a post-oxidation step, and the quantitative method to establish a comprehensive total MC detection approach applicable to surface water samples. The whole process included pretreatment using a freeze-drying method, purification using liquid-liquid extraction (LLE) for salt removal, and a comparison of quantitative methods using internal standards. Additionally, an evaluation of internal standards was conducted to assess availability during the oxidation process. In this study, an MMPB recovery rate of up to 50% was achieved, with an analysis precision of 14%. According to the results of QAQC, the satisfactory linearity of the calibration curve was a precision and the performance of the method for spiked samples was verified. The MMPB analysis method developed in this study showed relatively lower quantification limits and recovery rates than individual MC analysis methods. We believe these results stem from the inherent sensitivity differences between MCs and MMPB, as well as the complexity of the pre-treatment process centered around the oxidation process.