Doxorubicin (Dox) is an efficacious antineoplastic drug but is limited used for its cardiotoxicity. Histone Deacetylase 6 (HDAC6) has been indicated to participate in cardiomyopathies, however, its role in Dox-induced cardiac injury is largely unknown. In this study, we firstly aimed to determine the role of HDAC6 in Dox-induced cardiomyopathy. Immunoblotting revealed that Dox increased HDAC6 protein level and activity and decreased α-tubulin acetylation level in vitro and vivo. HDAC6 knockout (HDAC6−/−) mice showed obvious anti-Dox cardiotoxicity by conserved cardiac function monitored by echocardiography and the protection was reversed by Nocodazole, one drug lowering α-tubulin acetylation. Further mechanism investigation showed that improvement of mitochondria function and autophagy flux was partially inhibited by Nocodazole and Colchicine which lowers α-tubulin acetylation in neonatal rat cardiac myocytes. Aiming at transforming this research to clinical application, we then explored the effect of combined utilization of HDAC6 inhibitor and Dox on tumour and cardiac function. Results showed that Tubastatin A, one HDAC6 selective inhibitor, protected against Dox-induced acute cardiomyopathy without influencing the effect of Dox on inhibiting MDA-MB-231 subcutaneous tumour growth. These findings suggest a new treatment for cancer with Dox by combined utilization with HDAC6 selective inhibitors.