MC analysis of biological tissue is considered to be very difficult due to the lack of validated methods. This is the primary limiting factor for monitoring potential risks in both the flesh of aquatic organisms and the aquatic ecosystem. In this study, an effective method to determine free MCs (MC-LR and MC-RR) in the muscle and liver tissues of freshwater cultured fish was developed using solid-phase extraction (SPE) and liquid chromatography-tandem mass spectrometry (LC/MS-MS). The extraction solvent, time of extraction, eluent and purification of the extract were optimized. Various SPE cartridges were also investigated. In this optimized analytical procedure, an 85% methanol/water solution (v/v) was selected as the extraction solvent, after which the extracts were purified by removing fats and proteins; a HLB cartridge was chosen for MCs enrichment; and 90% methanol containing 0.02% formic acid/water solution (v/v) was used as the eluent. Under the optimized pretreatment conditions and instrument parameters, good recoveries of MC-LR and MC-RR were obtained at three concentrations (0.5, 1.0 and 2.0 µg g⁻¹ dry weight (DW)), with values ranging from 92.5 to 98.3% and 92.1 to 98.6%, respectively. The method detection limit (MDL) for muscle samples was 0.5 µg kg⁻¹ and 0.4 µg kg⁻¹ (DW) for MC-LR and MC-RR, respectively. The MDL for the liver samples was 0.8 µg kg⁻¹ (DW) for both MC-LR and MC-RR. The developed procedure was successfully applied to analyze MCs in the muscle and liver of fish samples collected from a Chinese freshwater aquaculture pond during bloom seasons. The MC-LR concentrations ranged from below the MDL to 4.17 µg kg⁻¹ and the MC-RR concentrations ranged from below the MDL to 2.64 µg kg⁻¹.