Ca2+ is an important messenger that affects almost all cellular processes. Ca2+ signaling involves events that happen at various time-scales such as Ca2+ diffusion, trans-membrane Ca2+ transport and Ca2+-mediated protein-protein interactions. In this work, we utilized multi-scale computational methods to quantitatively characterize Ca2+ diffusion efficiency, Ca2+ binding thermodynamics and molecular bases of Ca2+-dependent protein-protein interaction. Specifically, we studied 1) the electrokinetic transport of Ca2+ in confined sub-µm geometry with complicated surfacial properties. We characterized the effective diffusion constant of Ca2+ in a cell-like environment, which helps to understand the spacial distribution of cytoplasmic Ca2+. 2) the association kinetics and activation mechanism of the protein phosphatase calcineurin (CaN) by its activator calmodulin (CaM) in the presence of Ca2+. We found that the association between CaM and CaN peptide is diffusion-limited and the rate could be tuned by charge density/distribution of CaN peptite. Moreover, we proposed an updated CaM/CaN interaction model in which a secondary interaction between CaN’s distal helix motif and CaM was highlighted. 3) the roles of Mg2+ and K+ in the active transport of Ca2+ by sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) pump. We found that Mg2+ most likely act as inhibitor while K+ as agonist in SERCA’s transport process of Ca2+. Results reported in this work shed insights into various aspects of Ca2+ signaling from molecular to cellular level.