The traditional cylindrical fuel rods, with their heat uniformity, have been extensively studied in reactor core design. However, the relatively small contact area between the fuel rod and the coolant results in higher temperatures at the center of the rod. In this regard, the structural characteristics of the helical cruciform fuel rod effectively address this issue. Currently, most of the research on the helical cruciform fuel rods is in the aspect of thermal–hydraulic, while research on their neutron physical performance is limited. Therefore, the neutron physical performance of helical cruciform fuel rods is studied in this paper. In this study, based on the Direct Accelerated Geometry Monte Carlo, calculated and analyzed the effective neutron multiplication factors, variation in fuel mass and flux distribution of the helical cruciform fuel rods and the cylindrical fuel rods with equal volume and mass under different operating conditions. The results showed that the helical cruciform fuel rods with UO2 have higher initial reactivity and faster k_eff decline compared to other fuels. U–Mo alloy and U3Si2 offered superior neutron economy and reactivity retention. U–Mo alloy and U3Si2, with higher initial mass of U-235, showed significant U-235 depletion over 360 days, and demonstrated better neutron economy and reactivity retention. Besides, the helical cruciform fuel rods exhibited radially decreasing flux from the center outward, and showed similar symmetrical patterns across angular sectors. Among them, U–Mo alloy and U3Si2 fuel rods displayed smaller high-flux regions, reflecting lower overall flux and power.