Backgrounds: Although the OCT biometer using individual refractive index is available, comparisons of measurement value and intraocular lens (IOL) power calculation error with other SS-OCT biometers are not known. Objectives: To compare the new SS-OCT biometer ARGOS (OCTB1), which uses individual refractive indices to measure axial length, with the IOLMaster 700 (OCTB2) and OA-2000 (OLCR), which use equivalent refractive index. Method: Six hundred and twenty-two eyes of 622 patients who had been diagnosed with cataract were enrolled in the study. Among the 158 eyes that had undergone cataract surgery, the postoperative refractive error was evaluated using the Haigis formula. Results: The axial length measured by the OCTB1 showed a proportional bias in comparison with the other two biometers and a fixed bias in eyes with an axial length ≥26 mm. No significant difference was found in the median absolute refractive prediction error (p = 0.3278). However, in eyes with an axial length ≥26 mm, the OCTB1 showed myopic error compared with the other two biometers (p < 0.0001). Conclusions: In eyes with long axial length, when the conventional IOL calculation was optimized with the equivalent refractive index-based instrument, we need to consider that IOL calculation using OCTB1 tends to cause slightly myopic refractive prediction error.