M-type strontium hexaferrite nanocrystals of radar absorbing material (NRAM) i.e. SrFe12O19 were synthesized by modified flux method that combine the controlled chemical co-precipitation process for nucleation and complete uniform growth during annealing with NaCl flux. Uniform structural morphological transformation of nanocrystals from needle to hexagonal prism faces were noticed after annealing with increasing of heat treatment (HT) temperature from 800 to 1200°C for 4h. X-ray diffraction (XRD) results show the formation of various phases with increase in annealing temperature. The crystallinity and crystallite size are found to increase with increase in heat treatment temperature (15-40nm). The superparamagnetic behavior of strontium hexaferrite is confirmed by vibrating sample magnetometer (VSM) wherein it was noticed that magnetic field (10000 gauss max) did not have any effect on these materials. The transformation of magnetic properties i.e. from superparamagnetic to ferromagnetic behaviour after heating at various HT temperatures have been revealed by hysteresis loops under VSM study. The increase in saturation magnetization from 2.44 to 75.03 emu/gm is observed. Formation of ultrafine particles has been confirmed through field emission scanning electron microscope (FESEM). About 5 to10% of the needle like crystals in the ‘as synthesized’ condition were transformed to hexagonal pyramidal structure and most of the crystals are found to have plate like hexagonal structures with increase in heat treatment temperatures. The effect of such systematic morphological transformation of nanocrystals was observed in reflection loss properties in X band (8-12 GHz). The maximum reflection loss of -20.05, -24.31, -24.16, -25.22, -25.12, -24.01 dB at 8.1, 8.6, 9.2, 9.6, 10.7, and 12 GHz respectively are observed for the material heat treated at 1200°C. A significant increment from - 6.5 to -25.22 dB at 9.6 GHz in reflection loss (RL) is noticed due to symmetric morphological growth of RAM nanocrystal during annealing.