Development of highly sensitive and selective sensing systems of divalent zinc ion (Zn2+) in organisms has been a growing interest in the past decades owing to its pivotal role in cellular metabolism, apoptosis, and neurotransmission. Herein, we report the rational design and synthesis of a Zn2+ fluorescent-based probe by assembling lanthanide-doped upconversion nanoparticles (UCNPs) with chromophores. Specifically, upconversion luminescence (UCL) can be effectively quenched by the chromophores on the surface of nanoparticles via a fluorescence resonant energy transfer (FRET) process and subsequently recovered upon the addition of Zn2+, thus allowing for quantitative monitoring of Zn2+. Importantly, the sensing system enables detection of Zn2+ in real biological samples. We demonstrate that this chromophoreUCNP nanosystem is capable of implementing an efficient in vitro and in vivo detection of Zn2+ in mouse brain slice with Alzheimers disease and zebrafish, respectively.