Metal-organic frameworks (MOFs) are emerging nanomaterials with widespread applications for their superior properties. However, the potential health and environmental risks of MOFs still need further understanding. In this work, we investigated the toxicity of a typical cobalt-based MOF (ZIF-67) with varied primary particle sizes (100, 200, 400, 700 and 1200 nm) to Photobacterium Phosphoreum T3 strain, a kind of luminescent bacteria. The luminescence inhibition rate of all ZIF-67 nanoparticles (NPs) reached 40 % and higher at the concentration of 5 mg/L, exhibiting strong toxicity. Combined cellular assays and gene expression analysis confirmed that the general bioactivity inhibition and oxidative damage were induced mainly by ZIF-67 NPs, rather than Co2+ released from the ZIF-67 NPs. Additionally, the toxicity of ZIF-67 NPs demonstrated an evident size-dependent effect. For ZIF-67 smaller than 400 nm, the toxicity increased with the particle size decreased, while the trend was not significant when the particle size was larger than 400 nm. A potential explanation for this phenomenon is the smaller NPs (100 and 200 nm) may enter the cytoplasm, accumulating in the cytoplasm and causing more severe toxicity. Furthermore, Co2+ released from the ZIF-67 NPs was not the primary contributor to the toxic effect of ZIF-67 NPs which was verified by the toxicity results and the variation of toxicity-related indicators. These findings provided insight into the better design and safer use of MOFs, and it also implied the potential environmental risk of the MOF's cannot be ignored, especially for the bioapplication. Display omitted •Particle size-dependent toxicity of cobalt-based MOF was observed for Photobacterium phosphoreum T3 strain.•The difference in toxicity of the larger ZIF-67 NPs (>400 nm) was not significant.•Smaller ZIF-67 NPs (<400 nm) are more likely to cause the general bioactivity inhibition and oxidative damage.•Co2+ released from the ZIF-67 NPs not the sole contributor to the toxic effect of ZIF-67 NPs.