Background: Iron‐sulfur cluster assembly 1 (ISCA1) is an iron‐sulfur (Fe/S) carrier protein that accepts Fe/S from a scaffold protein and transfers it to target proteins including the mitochondrial Fe/S containing proteins. ISCA1 is also the newly identi‐ fied causal gene for multiple mitochondrial dysfunctions syndrome (MMDS). However, our knowledge about the physiological function of ISCA1 in vivo is cur‐ rently limited. In this study, we generated an ISCA1 knockout rat line and analyzed the embryo development. Methods: ISCA1 knockout rats were generated by replacing the exon1 of ISCA1 gene with the mCherry‐Cre fusion gene using CRISPR‐Cas9 technology. The ISCA1 expres‐ sion pattern was analyzed by fluorescence imaging using ISCA1 promotor driven Cre and mCherry expression. The embryonic morphology was examinated by microscope and mitochondrial proteins were tested by Western blot. Results: An ISCA1 knockout rat line was obtained, which expressed mCherry‐Cre fu‐ sion protein. Both of the fluorescence images from mCherry and Cre induced mCherry in a reporter rat strain, showing that ISCA1 expressed in most of the tissues in rats. The ISCA1 knockout resulted in abnormal development at 8.5 days, with a significant decrease of NDUFA9 protein and an increase of aconitase 2 (ACO2) in rat embryos. Conclusion: Deletion of ISCA1 induced early death in rats. ISCA1 affected the ex‐ pression of key proteins in the mitochondrial respiratory chain complex, suggesting that ISCA1 has an important influence on the respiratory complex and energy metabolism.