A field experiment was conducted to investigate differential effects of natural palygorskite (PAL) and its modified form (KH550-PAL) on the alleviation of heavy metals toxicity to tomatos grown in contaminated soil with Cd, Pb and Zn. Compared to heavy metal-contaminated soil without amendment, the application of natural palygorskite (PAL) or its modified form (KH550-PAL) significantly alleviated heavy metal toxicity to tomato. In addition, foliar malondialdehyde (MDA), hydrogen peroxide (H₂O₂) and superoxide (O₂^•–) contents as well as non-photochemical quenching (NPQ) reduced by 89, 28, 71, and 81%, respectively, in the modified palygorskite treatment than in the natural palygorskite treatment. Similar patterns were observed in heavy metals uptake of tomato. Foliar superoxide dismutase (SOD), catalase (CAT) and glutathione reductase (GR) activities increased by 228, 196 and 238%, respectively, in the modified palygorskite treatment than in the natural palygorskite treatment. Thus, the application of the modified form (KH550-PAL) significantly ameliorated the oxidative stress via enhancing antioxidant defense and reducing thermal dissipation, which further improved photosynthetic electron transport of photosystem II and biomass accumulation of tomato. However, the dose of the modified palygorskite (KH550-PAL) was not enough to buffer negative effects of heavy metal toxicity to tomato growth in the experiment. It is suggested that the amendment dose should be used with great care in remediating contaminated soils with heavy metals. Thus, further experiments are needed by different rates of the modified palygorskite (KH550-PAL).