Anthracycline induced cardiotoxicity, represented by Doxorubicin (DOX), is the main side effect limiting the use of anthracyclines as effective chemotherapeutic agents. These mechanisms have not been fully elucidated. It is necessary to refine the mechanisms of DOX cardiotoxicity and to develop drugs that can counteract DOX cardiotoxicity. In previous studies, the saffron extract was reported to successfully relieve DOX cardiotoxicity, but the mechanisms are unclear. First, we quantified 3423 proteins in the hearts of DOX group rats vs. control group rats using proteomics with high-sensitivity mass spectrometry to identify key proteins and signaling pathways. Furthermore, the important role of ribosomal proteins in the mechanism of DOX cardiotoxicity was revealed by the GEO transcriptome dataset and the literature on ribosomal protein ubiquitination. Second, we analyzed the key mechanisms and targets of saffron against DOX cardiotoxicity via 4D label-free proteomics. Through validation by ELISA, we identified the proteins XIRP2, EPHX1, SORBS2, CD81, FLOT2, FLOT1, CD59, DCN, CTSD and HSPA5 as critical targets of saffron extract against DOX cardiotoxicity. These discoveries have contributed to a deeper understanding of the mechanisms of DOX cardiotoxicity, as well as to the identification of the key therapeutic targets of saffron for preventing DOX cardiotoxicity.