A rapid, ultrasensitive, and high-throughput fluorimetric microarray method has been developed using hydrophobic pattern as the microarray substrate and 3-aminopropyltriethoxysilane-coupled carboxylic acid calcium (APS-CCA) as the fluorescent probes for sensing Ca2+ ions in blood. The hydrophobic pattern of the developed Ca2+ analysis microarray could largely suppress the “coffee-ring” effects to facilitate the better distribution density of testing microspots toward the high-throughput detections, and especially prevent the cross-contamination of the multiple samples between adjacent microspots. Moreover, the use of APS matrix could endow the CCA probe the enhanced environmental stability and fluorescence intensity, which is about 2.3-fold higher than that of free CCA. The interactions between APS-CCA and Ca2+ ions were systematically characterized by UV-vis and fluorescence measurements including microscopy imaging. It was demonstrated that the fluorimetric microarray could display the strong capacity of specifically sensing Ca2+ ions with the minimal interferences from blood backgrounds. Such an APS-CCA-based fluorimetric microarray can allow for the analysis of Ca2+ ions down to 0.0050 mM in blood, promising a highly sensitive and selective detection candidate for Ca2+ ions to be applied in the clinical laboratory.