In recent years, by using the etching techniques with great precision, the ion tracks in materials were converted into insulator and metal nanocapillaries. The physical and chemical properties of the inner surface on micro and nano-scales of these capillaries can be investigated by the interaction of ions with the surfaces. Stolterfoht et al. (2002 Phys. Rev. Lett. 88 133201) have found the evidence for capillary guiding in studying the transmission of 3 keV Ne7+ ions (energy/charge E/q100 kV) through the polymer nanocapillaries. The self-organized charge-up process was thought to inhibit close contact between the ions and the inner capillary walls. Skog et al. (2008 Phys. Rev. Lett. 101 223202) investigated the guiding effect of 7 keV Ne7+ ions (E/q100 kV) transmitted through SiO2 nanocapillaries, and found the evidence of sequentially formed charge patches along the capillary. For these keV highly charged ions with E/q100 kV, the charge patches were formed in a very short time, and then the repulsive electric field rapidly becomes strong enough to deflect the ions, then the ions move along the capillary axis without charge exchange. Zhou et al. (2016 Acta Phys. Sin. 65 103401) have investigated the transmission of 100 keV protons (E/q102 kV) through the nanocapillaries in polycarbonate (PC) membrane. It was found that the transmitted ions are located around the direction of the incident beam, rather than along the capillary axis. This indicated that the transmission mechanism of hundreds of keV protons through nanocapillaries is significantly different from that for keV highly charged ions. For 100 keV protons, several charge patches suppress the protons to penetrate into the surface, and the protons are transmitted via twice specular scattering near the surface and finally emitted along the incident direction. However, the study of the transmission of E/q101 kV ions through nanocapillaries is still lacking. In this work, we measure the time evolution of the relative transmission rate, charge state and angular distribution as well as the full width at half maximum of 20 keV protons (E/q101 kV) transmitted through the nanocapillaries in PC membrane at a tilt angle of +1. We observe a very long time pre-guiding period before the stable guiding process is established. During the pre-guiding period the direction of the transmitted H+ ions changes to the direction of capillary axis gradually. The transmitted H0 particles are composed of two peaks:the higher and sharper one is nearly in the beam direction, the wider and lower one is around the guiding direction. With the continuous charging-up process, the intensities of the narrow and sharp peak of transmitted H0 near the beam direction will decrease and disappear at the end. The data indicate that the scattering and guiding forces are both important for E/q101 kV ions during the period of pre-guiding process, and the guiding force is dominant till a long time pre-guiding period is ended. This finding will fill in the gap between E/q100 kV and 102 kV of previous studies of ions transmitted through nanocapillaries. It is also helpful for finding the applications of nano-and micro-sized ion beams produced by tapered glass capillary with E/q101 kV.