The peculiarities and modes of material modification with high-intensity, high-power density ion beams on the irradiated surface are studied for the first time. Chromium ions are implanted into a zirconium alloy using a 25 kW/cm2, 450 μs beam at the pulse repetition rates within 8–35 pps. Every high-energy ion pulse impact is followed by ultrafast cooling of the surface due to heat removal into the target material. Three modes are studied at the temperatures of 580, 700, and 900 °C with an additional pulsed heating. An increase in the average target temperature from 580 to 700 °C within 1 h at the same pulse power density allows increasing the depth of chromium ion alloying from 1.5 to more than 7 μm. The use of ultrafast cooling of the Zr1%Nb alloy surface offers a grain size reduction from a few μm to approximately 50–250 nm, without any microstructural changes throughout the sample volume. An inhomogeneous chromium ion distribution over the target surface and depth is observed.