Calcium ion is a versatile second messenger for diverse cell signaling in response to developmental and environmental cues. The specificity of Ca2+-mediated signaling is defined by stimulus-elicited Ca2+ signature and downstream decoding processes. Here, an Aequorin-based luminescence recording system was developed for monitoring Ca2+ in response to various stimuli in Arabidopsis. With the simple, highly sensitive, and robust Ca2+ recording, this system revealed stimulus- and tissue-specific Ca2+ signatures in seedlings. Cellular Ca2+ dynamics and relationship to Aequorin-based Ca2+ recording were explored using a GFP-based Ca2+ indicator, which suggested that a synchronous cellular Ca2+ signal is responsible for cold-induced Ca2+ response in seedlings, whereas asynchronous Ca2+ oscillation contributes to osmotic stress-induced Ca2+ increase in seedlings. The optimized recording system would be a powerful tool for the identification and characterization of novel components in Ca2+-mediated stress-signaling pathways.