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The aquatic toxicity and ecological risks of naphthenic acids (NAs) in marine environments have attracted an increasing amount of attention. However, there remains a lack of methodologies for the long-term risk assessment of NAs on marine ecosystems after high acid crude oil spill accidents. In this study, using the model microalgae Phaeodactylum tricornutum as the target object, the time-effect manner under NAs stress is investigated for a continuous 24–144 h. We found that: 1) NAs caused photosynthetic damage and persistent oxidative stress that slowed the growth rate and limited the maximum growth of P. tricornutum population within 24 h to 144 h of exposure, especially under the high concentration treatment; 2) Within 144 h, NAs can cause oxidative stress to P. tricornutum. The damage to cell membrane and radical oxidative species (ROS) accumulation of P. tricornutum were observed as obvious time-effect; 3) Under NAs stress, the two types of cell death (accidental cell death and regulated cell death) of P. tricornutum cell mediated by ROS played different roles in the population growth inhibition of P. tricornutum. Moreover, regulated cell death of the P. tricornutum cell was accompanied by PS externalization, DNA fragment and the G2/M phase stagnation acted as an adaptive regulatory mechanism under NAs stress. This explained the dose-time-effects of NAs on the population growth of P. tricornutum. Overall, the results suggested that NAs have a lasting effect on marine phytoplankton populations, and long-term risk assessments are required after high acid crude oil spill accidents. This is the first attempt to identify the different types of death at the cellular level to explain the time-effect toxicity at the population level of marine microalgae when exposed to NAs. This research will provide a new approach to facilitate further risk assessments for NAs and related contaminants in marine ecosystems. The toxic effects of naphthenic acids (NAs) on Phaeodactylum tricornutum were observed in consecutive 24–144 h. It was found that NAs has persistent photosynthetic damage and oxidative damage to P. tricornutum. Two different oxidative damage occurred in different time periods from 24 h to 144 h, causing accidental cell death and regulated cell death respectively. Two kinds of death together created the suppression of population density growth under the stress of NAs. [Display omitted] • Naphthenic acids caused photosynthetic damage and persistent oxidative stress. • Cell membrane damage and ROS accumulation showed time-effects. • ACD and RCD played different roles in population growth inhibition. • RCD acted as an adaptive mechanism that explained the dose-time effects of NAs. [ABSTRACT FROM AUTHOR]