Intracellular free Ca(2+) are canonically well known as significant "second messenger" in cells and regarded as critical regulators of bacterial metabolism. We investigated the influence of Ca(2+) dosage on the restoration of anammox consortium, in which nearly 80% cells were dead or badly damaged. Chemical analysis and flow cytometry (FCM) demonstrated that Ca(2+) dosage was of primary importance and the restoration process was apparently faster with increasing Ca(2+) as its concentration was ranged 0.02-0.5mM in feeding. Using FCM and Fura red fluorescence labeling for analysis of intracellular free Ca(2+), we found a strong correlation between external Ca(2+) concentration in feeding and the levels of steady-state intracellular free Ca(2+), the abundance of which was considered as the intrinsic causes for favoring anammox consortium restoration. This study provides new insight into the ions effects on rapid restoration of damaged anammox consortium, targeting efficient nitrogen removal from wastewater with anammox process.