A new chemosensor, namely N-(2-morpholinoethyl)acetamide-4-morpholine-1,8-naphthimide (MMN), was designed and synthesized through an amidation reaction. MMN was fabricated as a multifunctional fluorescent probe for monitoring pH and isoxaflutole. MMN exhibited excellent stability in MeCN/H2O (v/v, 9/1), with an obvious “off–on” fluorescence response toward pH changes due to intramolecular charge transfer (ICT), where the linear response ranges of MMN in the weakly acidic system were from 4.2 to 5.0 and from 5.0 to 6.0 with apparent pKa = 4.62 ± 0.02 and 5.43 ± 0.02. Based on morpholine as the lysosome targetable unit, MMN could selectively locate lysosomes in live cells. MMN also successfully detected the presence of H+ in test papers. Finally, MMN could specifically recognize isoxaflutole at a detection limit of 0.88 μM. A possible sensing mechanism was identified based on density function theory calculations. These results indicate that MMN could be a superior potential chemosensor for detecting pH and isoxaflutole selectively and sensitively and could be used in real sample detection.