Two 3-hydroxyflavone derivatives as one- and two-photon fluorescent chemosensors for cysteine (Cys) and homocysteine (Hcy) were synthesized. The recognition properties and mechanism of the chemosensors for Cys and Hcy were investigated systematically. The experiment results indicate that 3-hydroxyflavone compound 1 (6-bromo-2-(9-ethyl-9H-carbazol-3-yl)-3-hydroxy-chromen-4-one) after the addition of nickel ions exhibits good recognition properties for Cys and Hcy with fluorescence enhancement and 65nm absorption peak blue shift based on nickel displacement reaction mechanism. The detection limits (DL) with fluorescence as detected signal are 4.06 × 10µM (Cys, linear range of 10-80µM) and 5.8 × 10µM (Hcy, linear range of 10-100µM), respectively. But acrylate substituted 3-hydroxyflavone compound 2 (4-oxo-2-(4-diethylamino-phenyl)-4H-chromen-3-yl acrylate) can specially identify Cys with fluorescence turn-on (DL = 1.87 × 10µM, linear range of 4-22µM) based on Cys leading to acrylate hydrolysis mechanism and succedent excited-state intramolecular proton transfer process of 3-hydroxyflavone compound. Then Cys and Hcy biological thiols can be recognized at one time by these two 3-hydroxyflavone derivatives. The bioimaging experiment indicates that both the compounds can be successfully applied to the detection of Cys/Hcy in living cells and compound 2 also can be applied to bioimaging Cys in zebrafish by one- and two-photon fluorescence mode. Then these two compounds have a potential in the application of biological sample analysis.