Cu-SSZ-13 zeolite has attracted great interest owing to its extraordinary performance in the selective catalytic reduction of NOx with NH3 (NH3-SCR); however, the high expense in the costly templates for synthesizing SSZ-13 remains a serious obstacle for its application in large scale, which exacts alternative methods to get SSZ-13 of high performance in NH3-SCR at reduced cost. In this work, a series of methods, including the interzeolite conversion from X and Y zeolites (to get SZ-XC and SZ-YC, respectively) and the assistance with seed crystal and fluorine ion (to get SZ-S and SZ-F, respectively), were used to synthesize the Al-rich Cu-SSZ-13 zeolites; the influence of preparation method on the Al distribution, hydrothermal stability and catalytic performance of Cu-SSZ-13 in NH3-SCR was then comparatively investigated. The results indicate that the Cu-SSZ-13 zeolites prepared by various methods are also rather different in the content of paired Al and active Cu2+-2Al species, following the order of SZ-F > SZ-S > SZ-YC > SZ-XC; a positive correlation is observed between the catalytic activity in NH3-SCR and the content of α-Cu2+-2Al species determined by the electron spinning resonance. In particular, the Cu-SSZ-13 zeolite prepared by using fluoride as an assistant (Cu-SZ-F) has much higher fraction of paired Al and active α-Cu2+-2Al species and thereby exhibits better catalytic performance in NH3-SCR, with an NO conversion of nearly 80% at 200 °C under a gaseous hourly space velocity (GHSV) of 240,000 h−1. Moreover, the Cu-SSZ-13 zeolite prepared by the fluoride assistance method also displays less silanol defects and greater hydrothermal stability, showing enormous potential as a practicable catalyst of low cost in the elimination of NOx by NH3-SCR.