Chlorine (Cl) is indispensable for the growth of plants. While rarely systematic reports are available for the effect of Cl-containing fertilizers on citrus production. This study aimed to investigate the impacts of various Cl-containing fertilizers on the nutrients in the leaves, the yield and quality of sweet orange, and the Cl migration in the plant–soil–leaching system. A 5-year field experiment (2016–2020) with five Cl treatments (0, 75, 150, 450, and 900 kg ha−1), and soil core lysimeter test with five Cl levels (0, 150, 225, 300, and 450 kg ha−1) were carried out. The results showed that 77.0% of Cl leached into above 60 cm deeper soil layer, with calcium as the main accompanying ions, resulting in less Cl being absorbed by the citrus plants. The content of Cl in the leaves and soil was enhanced by the increasing input of Cl-containing fertilizer, without yearly increased characteristics, under a mean annual rainfall of 1,474 mm. Chlorine significantly increased the yield (13.24–37.8 9%), fruit weight, and vitamin C (Vc), in addition to enhancing the flavor and the juice yield of sweet orange via improving the absorption of N and K. Moreover, the long-term application of potassium sulfate has elevated the accumulation of sulfur in the soil and in leaves; it is becoming a potential risk factor for citrus production. Taken together, the application of Cl-containing fertilizer in sweet orange is feasible, and trace absorbance of Cl could improve the yield and fruit quality of sweet orange.