Mitochondrial dysfunction is a fundamental challenge in septic cardiomyopathy. Mitophagy and the mitochondrial unfolded protein response (UPR
mt
) are the predominant stress-responsive and protective mechanisms involved in repairing damaged mitochondria. Although mitochondrial homeostasis requires the coordinated actions of mitophagy and UPR
mt
, their molecular basis and interactive actions are poorly understood in sepsis-induced myocardial injury. Our investigations showed that lipopolysaccharide (LPS)-induced sepsis contributed to cardiac dysfunction and mitochondrial damage. Although both mitophagy and UPR
mt
were slightly activated by LPS in cardiomyocytes, their endogenous activation failed to prevent sepsis-mediated myocardial injury. However, administration of urolithin A, an inducer of mitophagy, obviously reduced sepsis-mediated cardiac depression by normalizing mitochondrial function. Interestingly, this beneficial action was undetectable in cardiomyocyte-specific FUNDC1 knockout (FUNDC1
CKO
) mice. Notably, supplementation with a mitophagy inducer had no impact on UPR
mt
, whereas genetic ablation of FUNDC1 significantly upregulated the expression of genes related to UPR
mt
in LPS-treated hearts. In contrast, enhancement of endogenous UPR
mt
through oligomycin administration reduced sepsis-mediated mitochondrial injury and myocardial dysfunction; this cardioprotective effect was imperceptible in FUNDC1
CKO
mice. Lastly, once UPR
mt
was inhibited, mitophagy-mediated protection of mitochondria and cardiomyocytes was partly blunted. Taken together, it is plausible that endogenous UPR
mt
and mitophagy are slightly activated by myocardial stress and they work together to sustain mitochondrial performance and cardiac function. Endogenous UPR
mt
, a downstream signal of mitophagy, played a compensatory role in maintaining mitochondrial homeostasis in the case of mitophagy inhibition. Although UPR
mt
activation had no negative impact on mitophagy, UPR
mt
inhibition compromised the partial cardioprotective actions of mitophagy. This study shows how mitophagy modulates UPR
mt
to attenuate inflammation-related myocardial injury and suggests the potential application of mitophagy and UPR
mt
targeting in the treatment of myocardial stress.