<p>All life processes depend on the precise spatiotemporal expression of genes, which involves orderly processes including transcription, posttranscriptional processing, translation, and posttranslational modification. Accumulating evidence demonstrates that Ca²⁺ is the most critical second messenger that orchestrates nearly all fundamental biological processes vital for maintaining normal physiological functions. Ca²⁺ homeostasis/signaling is primarily maintained through Ca²⁺ influx, cytoplasmic Ca²⁺ release, Ca²⁺ store cycling, and binding and release of Ca²⁺ buffers. Their coordinated interactions ensure that Ca²⁺ concentrations remain within the physiologically appropriate range. Ca²⁺ signaling must be appropriately activated or suppressed during cellular signal transduction to support specific functions, and its dysregulation can trigger various pathological conditions. This review summarizes recent progress in Ca²⁺ signaling regulatory networks, including the roles of key regulatory elements/toolkits, the functional significance of Ca²⁺ signals in different microdomains, and the influence of Ca²⁺ signaling on gene expression, along with the underlying mechanisms at various stages of gene expression. The involvement of Ca²⁺, both independently and collaboratively, in the nucleus, cytoplasm, subcellular microdomains such as mitochondria, and the extracellular space, in the multi-level regulation of gene expression, has been extensively studied. This information is essential for understanding the mechanisms underlying gene expression and for advancing the diagnosis and treatment of diseases. Finally, we propose forward-looking recommendations to address current research gaps, aiming to provide valuable references for researchers in this field.</p> Graphical abstract <p></p>