In this study, various pre-treatment methods were evaluated for microalgae separation. These methods aimed to facilitate safe, rapid, and cost-effective online imaging for real-time observation and cell counting. As pre-treatment techniques, heating, chemical hydrolysis, heating combined with chemical hydrolysis, and sonication were employed. The effectiveness of these methods was evaluated in the context of online imaging quality through experimentation on cultivated microalgae (Chlorella vulgaris and Scenedesmus quadricauda). The chemical treatment method was found to be inappropriate for improving image acquisition. The heating pre-treatment method exhibited a drawback of prolonged cell dispersion time. Additionally, the heating combined with chemical hydrolysis method was confirmed to have the lowest dispersion effect for Chlorella vulgaris. Conversely, ultrasonication emerged as a promising technique for microalgae separation in terms of repeatability and reproducibility. This study suggests the potential for selecting optimal pre-treatment methods to effectively operate real-time online monitoring devices, paving the way for future research and applications in microalgae cultivation and imaging.