<p>Cancer is one of the most significant public health challenges in the new millennium, and complex mechanisms are at work to contribute to its pathogenesis and progression. The Wnt signaling pathways, which are crucial conserved cascades involved in embryological development and tissue homeostasis, and mitochondria, the intracellular powerhouses responsible for energy production, calcium and iron homeostasis, as well as mitochondrial apoptosis in eukaryotic cells, have their own mechanisms regulating these pathological processes. In the past decade, accumulating evidence has indicated that Wnt signaling pathways directly regulate mitochondrial biogenesis and function under physiological and pathological conditions. In this review, we systemically summarize the current understanding of how Wnt signaling pathways, particularly the canonical Wnt cascade, regulate mitochondrial fission, respiration, metabolism, and mitochondrial-dependent apoptosis in cancer. In addition, we discuss recent advancements in the research of anticancer agents and related pharmacological mechanisms targeting the signaling transduction of canonical Wnt pathway and/or mitochondrial function. We believe that the combined use of pharmaceuticals targeting Wnt signaling and/or mitochondria with conventional therapies, immunotherapy and targeted therapy based on accurate molecular pathological diagnosis will undoubtedly be the future mainstream direction of personalized cancer treatment, which could benefit more cancer patients.</p> Graphical abstract <p></p>