FER zeolites have a unique framework structure and acid distribution, and are widely studied as a catalyst for reactions such as n-butene skeletal isomerization and dimethyl ether carbonylation. The Brönsted acid site (BAS) located in the 10-member ring (10-MR) of FER zeolites serves as the active site for the isomerization reaction of skeletal n-butene to produce isobutene. This study prepared five types of FER zeolites using different methods: using pyrrolidine (PY) alone as a template; using Na-form FER as seeds (SN) or H-form FER as seeds without organic structure directing agents (OSDAs); and combining the seeds of SN or SH with PY as OSDAs. The differences in the structure and acid distribution of the five zeolites were investigated, as well as their catalytic performance for the skeletal isomerization of n-butene. Experiments and characterization results showed that under hydrothermal synthesis conditions, the FER-PY+SH zeolites synthesized by using both H-form zeolites seeds and pyridine exhibited the highest aluminum concentrations at T1 and T3 sites, along with the greatest BAS located in the 10-MR. This unique composition contributed to the highest selectivity of isobutene. The FER-PY+SH catalyst was continuously used for 720 h at 350 °C, 0.1 MPa, and an n-butene mass space velocity of 2.0 h−1 for three cycles of 2160 h. During this period, the conversion of n-butene was over 39%, while the selectivity of isobutene exceeded 95%. The FER-PY+SH catalyst exhibited excellent stability and activity.