Neuroinflammation can result in common neurodegenerative diseases, such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). As the primary immune cells of the central nervous system, microglia will be over-activated and pro-inflammatory mediator nitric oxide (NO) would excessive accumulation. Therefore, inhibition of the over-generation of NO in microglia has been shown to delay the progress of such disorders 1-3. Marine-derived fungi have proven to be a research hotspot for searching effective secondary metabolites due to that fungi would adapt to thrive under extreme environments 4. In our previous study, the fungus Aspergillus aculeatus obtained from a sponge Callyspongia sp. attracted our attention due to its resistance and survival rates under exogenous Nitric Oxide stress. In this approach, metabolomic analysis using UHPLC-HRMS based analytical techniques were applied to characterize the difference of secondary metabolites of A. aculeatus with or without NO stress. The result showed that some bis-indole alkaloids could be used as potential Q-markers to distinguish the strain under this stress from the control group. And this founding suggested indole-alkaloids from this genus would throw the light for neuroinflammation-related diseases.