Lime juice is rich in bioactive components and exerts a wide range of therapeutic effects, especially antioxidant activity. Freeze concentration is considered an essential method to maintain the nutritional values and bioactives of fruit juices. This study aimed to compare the ability in enriching ascorbic acid, total phenolic compounds, and major flavonoids and the antioxidant activity (DPPH) of concentrated lime juices prepared by vacuum and freeze-concentrations. The ascorbic acid in the juices was analyzed using the HPLC-PDA method. The total phenolic content and DPPH inhibition ability were measured by the colorimetric method. The polyphenol profiles of two lime varieties (C. latifolia and C. limonia) were qualitatively analyzed using LC-TOF MS/MS; then, the major juices’ flavonoids were analyzed by HPLC-PDA against/based on commercial standards. The results showed that C. latifolia was superior to C. limonia in ascorbic acid, TPC, major flavonoids, and antioxidants. C. latifolia was also more diverse than C. limonia in its polyphenol profile through the identified compounds (18 vs. 15). Freeze-concentrated lime juices were significantly higher than the vacuum-concentrated counterparts in ascorbic acid (mean difference from 9.41 to 22.01 mg, p < 0.01), and TPC (from 60.76 to 149.88 mgGAE). The quantification of major flavonoids showed that the freeze-concentrated lime juices retained high levels of hesperidin, eriocitrin, and rutin (p < 0.01) whereas the vacuum concentration preserved higher ones in diosmin and naringin (p < 0.01). The freeze-concentrated lime juice was significantly higher than vacuum-concentrated lime juices in the DPPH scavenging activity by at least 15% (p < 0.01). Overall, freeze concentration enriched bioactive compounds in lime juices almost threefold and improved antioxidants at least twofold. Thus, freeze concentration is promising for the industry in producing high-quality lime juice to preserve its thermal liable bioactive component.