Adenosine triphosphate (ATP), as an important intracellular energy currency produced in mitochondria, is closely related to various diseases in living organisms. Currently, the biological application of AIE fluorophore as a fluorescent probe for ATP detection in mitochondria is rarely reported. Herein, D−π−A and D−A structure-based tetraphenylethylene (TPE) fluorophores were employed to synthesize six different ATP probes (P1−P6), and the phenylboronic acid groups and dual positive charge sites of probes could interact with the vicinal diol of ribose and negatively charged triphosphate structure of ATP, respectively. However, P1 and P4 with a boronic acid group and a positive charge site had poor selectivity for ATP detection. In contrast, P2, P3, P5, and P6 with dual positive charge sites exhibited better selectivity than P1 and P4. In particular, P2 had more advantages of high sensitivity, selectivity, and good time stability for ATP detection than P3, P5, and P6, which was ascribed to its D−π−A structure, linker 1 (1,4-bis(bromomethyl)benzene), and dual positive charge recognition sites. Then, P2 was employed to detect ATP, and it exhibited a low detection limit of 3.62 μM. Moreover, P2 showed utility in the monitoring of mitochondrial ATP level fluctuations.