Zeolites with intergrown structures are particularly interesting because they often exhibit unique performance in heterogeneous catalysis. This raises the bar of the structural characterizations and remains an enormous challenge to understand the synthesis conditions and the formation mechanisms of such intergrown materials. Herein, a novel intergrown zeolite (ECNU-5) was successfully synthesized via a rapid dissolution-recrystallization (RDR) route, which reorganized the conventional MWW layer stacking into two new different polymorphs, ECNU-5A and ECNU-5B. Structure elucidation indicates both polymorphs are reconstructed from the same MWW layer but are different in relative shift between adjacent layers. ECNU-5 is the first structure-determined zeolite with interrupted structure that MWW layers shift in the horizontal direction, in which the two polymorphs are never predicted before and are additional members of the MWW family. The unique geometry mismatch between the organic structure-directing agent (OSDA) and inorganic silicate framework is ascribed to causing the zeolite layer shift. Moreover, the implementation of silylation technique readily expanded the interlayer pore of as-made ECNU-5, producing the interlayer-expanded zeolite (IEZ-ECNU-5), which maintained the original stacking sequence of MWW sheets.