Abstract Understanding organelle interactions is crucial for unravelling the cellular mechanisms underlying apoptosis, particularly in cancer therapy. Microtubules provide structural and functional support to organelles, and their disruption can cause irreversible damage, triggering cell death. Mitochondria rely on the microtubule network for transport, positioning, and maintaining their structural integrity. Colchicine, a potent microtubule‐depolymerizing agent, disrupts this network by inhibiting tubulin polymerization. When microtubules disassemble, mitochondria lose their organization, experience stress, and undergo fragmentation and dysfunction. Building on this, we developed a non‐cleavable linker connecting colchicine with three fluorophores: an ER‐targeting coumarin ( CC ), a non‐specific dansyl ( DC ), and a mitochondrial‐targeting pyridinium ( PC ), which emit in the blue, green, and red regions, respectively. PC specifically stains mitochondria, induces apoptosis by disrupting the microtubule network, and leads to cell death (IC 50 – 0.54 µM). PC also enables real‐time study of microtubule depolymerization and organelle crosstalk. The confocal fluorescence imaging captured time‐lapse interactions between microtubules and mitochondria, providing valuable insights into the underlying mechanistic processes.