Various acid-base molecular clusters involving organic species can serve as precursors that play important roles in the formation of an atmospheric aerosol. Due to its structural flexibility and its ability to form multiple hydrogen bonds, citric acid acts as a key species in forming clusters that are critical in the nucleation of related aerosol precursors. Thus, it is provoking to characterize the structures of these clusters at the molecular level. In this paper, protonated citric acid-ammonia clusters of various sizes were generated by electrospray ionization and studied by tandem mass spectrometry. The structures of [(CA)2+NH4]1+ and [(CA)4+NH4]1+ were further characterized by the method of infrared photodissociation (IRPD) spectroscopy. Combined with theoretical calculations, it is found that the most stable structures of the dimeric and tetrameric isomers show the shapes of an ingot and a lantern, respectively. It has been revealed that the temperature has a great effect on the contributions of different isomers for both dimers and tetramers. The dominat isomers are found to have more open structures at higher temperatures, facilitating the growth of clusters through new hydrogen bonds.