Microcystin-LR (MC-LR) generated by cyanobacteria is a kind of potent hepatotoxin, which poses a considerable threat to human health. In the research field of MC-LR removal, the quantitative analysis in a wide concentration range of samples is inevitable. In this paper, we presented the pseudo united use of an Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC-MS) and High Performance Liquid Chromatography system with a Variable Wavelength Ultraviolet Detector (HPLC-VWD) approach to detect MC-LR. The UPLC-MS system was applied to determine MC-LR in trace concentration because of its high sensitivity. However, it is generally believed that the determination of high concentration samples by UPLC-MS will cause problems such as inaccurate quantification and contamination of ion sources. In consequence, the HPLC-VWD was employed to determine the high concentration of MC-LR. The sensitivity, precision and accuracy of the two methods were compared in detail. The linear ranges of UPLC-MS and HPLC-VWD methods were from 0.08 to 10 μg L⁻¹ and 1 to 5000 μg L⁻¹, respectively. The detection and quantification limits of UPLC-MS were 0.03–0.05 μg L⁻¹ and 0.08 μg L⁻¹, and the corresponding two values of HPLC-VWD were 0.6 and 1.0 μg L⁻¹. The recoveries of UPLC-MS and HPLC-VWD were 88.5–106.7% and 98.7–101.6%, with the relative standard deviations of 3.72–5.45% and 0.38–1.69%, respectively. The potential adsorption properties of MC-LR on filter membranes with diverse materials and pore sizes were evaluated and the negative results were obtained. The detection of MC-LR by UPLC-MS was free from matrix effects. The presented UPLC-MS and HPLC-VWD methods were used to analyze the water samples from Erhai Lake, which is located in Dali, Yunnan, China. The results of UPLC-MS analysis indicated that the MC-LR was only identified in water samples of Shuanglang Bay and Xier River, with concentrations of 0.120 and 0.303 μg L⁻¹, whereas MC-LR was not detected by HPLC-VWD.