Global warming has facilitated the expansion of the invasive cyanobacterium Raphidiopsis raciborskii to higher latitudes， while current studies on bloom control methods for this species remains limited. This study evaluated the algicidal effects of two amino acid analogs， L-3，4-dihydroxyphenylalanine （L-DOPA） and homoarginine （Har）， on R. raciborskii and investigated their physiological impacts. Results showed that both compounds significantly induced reactive oxygen species （ROS） accumulation， with L-DOPA exhibiting stronger ROS stimulation than Har. Both analogs damaged the photosynthetic system: L-DOPA impaired the photosystem reaction centers， electron transport chain， and chlorophyll a （Chl.a）， while significantly reducing phycobiliprotein （PBP） content but increasing the proportions of allophycocyanin （APC） and phycoerythrin （PE）. L-DOPA treatment caused severe filament fragmentation （average length reduced to 9.70% of the control） and extensive cellular damage. In contrast， Har damaged the photosystem reaction centers and electron transport chain but promoted PBP synthesis and PE proportion， resulting in moderate filament breakage （22.33% of the control） and significant extracellular polymeric substance （EPS） secretion. This study demonstrates that both Har and L-DOPA effectively inhibit R. raciborskii， with L-DOPA exhibiting stronger algicidal activity， indicating that the two amino acid analogs exhibit distinct algicidal mechanisms. Our findings provide fundamental data for developing novel cyanobacterial bloom control technologies.