Natural zeolite and kaolin are abundant in Indonesia especially in Java and Belitung islands. These materials generally contain high aluminosilicate minerals that can be used as silica and alumina sources for the formation of NaY zeolite. This research aimed to identify the modification of NaY zeolite structure using Bayat natural zeolite as alumina source and Belitung kaolin as silica source and its catalytic activity for n-hexadecane cracking. Pretreatment of materials were performed in several steps: activation, purification, fragmentation for Bayat–Klaten natural zeolite, and silica extraction for Belitung kaolin. The synthesis of NaY was performed hydrothermally using seed-assisted method with crystallization times of 24 and 48 h. The surface area analysis showed a typical surface area of microporous zeolite (i.e., a pore diameter of 1.897 nm) and surface area of 309.4 cm2/g. Meanwhile, powder X-ray diffraction characterization showed that the as-synthesized materials have the structure of NaY zeolite. The optimum crystallization time was 24 h with Si/Al ratio of 4.10. Furthermore, both synthetic and natural sourced NaY zeolites were converted into HY zeolites and employed as cracking catalyst of n-hexadecane in a fixed-bed reactor at 500 °C for 75 s. The natural sourced HY resulted in 59.80% conversion and 59.80% yield of gasoline product (C9–C12). These values were lower than the results given by synthetic HY (80%).