Excessive levels of cyanide (CN−) and hypochlorite (ClO−) anions are the significant threats to the human health and the environment. Thus, great efforts have been to design and synthesize molecular sensors for the simple, instantaneous and efficient detecting environmentally and biologically important anions. Currently, developing a single molecular sensor for multi-analyte sensing is still a challenging task. In our present work, we developed a new molecular sensor (3TM) based on oligothiophene and Meldrum's acid units for detecting cyanide and hypochlorite anions in biological, environmental and food samples. The detecting ability of 3TM has been examined to various testing substances containing amino acids, reactive oxygen species, cations and anions, showing its high selectivity, excellent sensitivity, short response time (ClO−: 30 s, CN−: 100 s), and broad pH working range (4–10). The detection limits were calculated as 4.2 nM for ClO− in DMSO/H2O (1/8, v/v) solution and 6.5 nM for CN− in DMSO/H2O (1/99, v/v) solution. Sensor 3TM displayed sharp turn-on fluorescence increasement (555 nm, 435 nm) and sensitive fluorescence color changes caused by CN−/ClO−, which is ascribed to the nucleophilic addition and oxidation of ethylenic linkage by cyanide and hypochlorite, respectively. Moreover, sensor 3TM was applied for hypochlorite and cyanide detecting in real-world water, food samples and bio-imaging in live cells and zebrafish. To our knowledge, the developed 3TM sensor is the seventh single-molecular sensor for simultaneous and discriminative detecting hypochlorite and cyanide in food, biological and aqueous environments using two distinct sensing modes.