A high-silica zeolite ECNU-13 (Si/Al=23) with a new three-dimensional (3D) pore system and a nanosized morphology has been developed, consisting of multitudes of 10-membered ring (10-R) medium pores and one set of 8-R small pores. A phase-discrimination strategy was proposed to synthesize ECNU-13 by regulating the gel compositions and nucleation processes that were used for preparing 12-R large-pore germanosilicate IM-20 with the known UWY topology. The crystallization was directed towards forming one set of single four-ring (s4r) composite building units together with one set of double four-ring (d4r) rather than two different types of d4r units in IM-20. The electron crystallographic investigations elucidated that the ECNU-13 structure was composed of two kinds of polymorphs as a result of distinct atomic positionings in s4r units. In catalytic cracking of 1-butene, ECNU-13 exhibited high propene selectivity (55.6 %) and propene to ethylene molar ratio (>4.7) superior to well-studied conventional ZSM-5 zeolite catalyst.