Toxic harmful algal blooms (HABs) have received increasing attention owing to their threat to the health of aquatic life and seafood consumers. This study evaluated the impacts of elevated atmospheric partial pressure of CO2 (pCO2) on the production of paralytic shellfish toxins (PSTs) in different Alexandrium spp. strains, together with its further effects on the bioaccumulation/elimination dynamics of PSTs in bivalves contaminated with PSTs from toxic dinoflagellates. Our results showed that elevated pCO2 stimulated the growth of the two Alexandrium spp. (A. catenella and A. pacificum) isolated from the northern and southern coastal areas of China, respectively, and affected PST production including content and toxicity of the two strains differently. Further PSTs bioaccumulation/elimination in PSTs-contaminated Manila clam, Ruditapes philippinarum under high pCO2 also occurred. It is worth noting the biotransformation of neosaxitoxin (NEO) with high toxicity through trophic transfer with effect of elevated pCO2. When in microalgae cultured under the control (410 ppm) and elevated pCO2 conditions (495 and 850 ppm), the proportion of NEO in the PST content produced by A. catenella was reduced from 11.1 to 6.4 and 2.6 %, while the proportion of NEO in A. pacificum was increased from 3.1 to 3.6 and 4.7 %, respectively. NEO accounted for >50 % of total PST contents in clams, which were biotransformed via transfer from dinoflagellates and higher pCO2 enhanced this biotransformation leading to increased NEO accumulation. The negatively affected elimination of PSTs, especially NEO, in clams fed with A. catenella or A. pacificum, indicates that the detoxification of PSTs-contaminated clams may be more difficult under elevated pCO2. This study provides reference for developing models to assess the safety of bivalves under the co-stress of environmental change and toxic HABs, suggesting that ocean acidification may lead to the higher safety risk of Manila clams exposed to toxic HAB dinoflagellates.