Okadaic acid (OA), dinophysistoxin-1 (DTX1), dinophysistoxin-2 (DTX2), yessotoxin (YTX), 1-homoyessotoxin (hYTX), pectenotoxin-2 (PTX2), azaspiracid-1 (AZA1), azaspiracid-2 (AZA2), azaspiracid-3 (AZA3), pinnatoxin-G (PnTX-G), spirolide (SPX1) and gymnodimine (GYM) are lipophilic marine toxins (LMTs), which are harmful to humans and also possess potential therapeutic applications. To compare the toxicity and medical value of LMTs, Neuro-2a, NG108-15 and MCF-7 cell lines were employed to test cytotoxicity under the same conditions and toxin concentrations. These results showed OA, DTX1, DTX2, YTX, hYTX, PTX2, AZA1, AZA2 and AZA3 were cytotoxic in all tested cell types. However, PnTX-G, SPX1 and GYM had no effect on the three cell lines at 0.01-1000 nM. The sensitivity sequences based on EC50 values of the three cell lines to OA, DTX1, DTX2, YTX, hYTX, PTX2, AZA1, AZA2 and AZA3 were confirmed at 24 h and 48 h of exposure. Neuro-2a cell line was sensitive to AZA3, AZA2, AZA1; NG108-15 to YTX, hYTX and PTX2; and MCF-7 to DTX1. These data provided a scientific basis for calculating the toxicity equivalency factors (TEFs) of the OA, DTX1, DTX2, YTX, hYTX, PTX2, AZA1, AZA2 and AZA3 based on cytotoxicity, and possess an application value for further development of anti-tumor drugs.