The artificial cultivation of Mengzi pomegranate has been conducted on a large area for more than 30 years in Yunnan, China. As the quality of pomegranate cultivars have degraded seriously, new cultivars have gradually been introduced to meet market demand. Comparative quality evaluation of different pomegranate varieties is beneficial to guide cultivar improvement and cultural program modification. The present study investigated the differences of physicochemical characteristics of the introduced Tunisian soft-seed pomegranate in different climate zones in Yunnan, China. Meanwhile, the differences between native cultivars (Tian guan yan (TGY) and Tian lv zi (TLZ)) and introduced cultivar were also compared. It was found that the Tunisian soft-seed pomegranate grown in Huize (Tunisian pomegranate in Huize, TH) in the temperate plateau monsoon climate belt had the highest fruit weight, % of seed, TAC, TPC, TSS, amino acids, and Mn, and had the lowest organic acids and Na. While grown in the subtropical monsoon climate area Shiping (Tunisian pomegranate in Shiping, TS), the Tunisian pomegranate fruits had the highest amounts of Cu. Commonly, there were significant correlations between cultivation climate regions and fruit properties. The contents of the TSS, TAC, TPC, flavor amino acids and organic acids varied with planted climate zones. The introduced Tunisian soft-seed pomegranate has comparable levels of physicochemical characteristics with the local main cultivars in the same planted climate region. Tunisian soft-seed pomegranate of higher quality can be obtained in Huize area. Collectively, the climate difference and cultivar shift have a significant effect on pomegranate production in Yunnan, and pomegranate with good quality can be obtained by using proper cultivars in optimized climate zone.