To verify whether there is a non-thermal effect in the radio frequency (RF) treatment process, it's very important for effectively excluding the thermal effect. Native maize starch (MS) slurry was treated under a specific electric field intensity while maintaining the sample temperature at 25 ± 2 °C for different times (1, 2, 4 and 8 h), which would effectively eliminate the influence of thermal effect on starch. A corresponding low electric field intensity of 3.3–3.4 kV/m was established after adjusting the electrode gap to be 220 mm of the 27.12 MHz RF system. Samples treated without RF-wave for the same time (1, 2, 4 and 8 h) were used as controls. The differences between the effect of these two treatments on the multi-scale structural and gelling properties of starch samples were investigated. Results showed that the low intensity RF-wave treatment enhanced the short-range structural order. A higher degree of order value and the double helical structure were observed from Fourier transform infrared (FTIR) spectra and solid state 13C nuclear magnetic resonance (13C NMR). Moreover, compared to control MS, the crystallinity of low intensity RF-treated starch significantly increased though the crystal pattern remained unchanged. Low intensity RF-wave treated starch had no significant difference in loss modulus, energy and distance of inter-double helices hydrogen bond, and pasting properties (i.e. TV, SB and BD) when compared with control sample. The effect of low intensity RF wave on starch without heating was insufficient to cause macroscopic property changes. These results provide valuable insights into the structural changes of starch treated by low intensity RF-wave and verify that the non-thermal effect of RF waves may be primarily achieved through the dipole polarization mechanism.