Deepak Suthar One often forgotten point is the tiny amount of sample measured in SEM. Try calculating the amount for interest. Heterogeneity of the sample explains the rest.
As Nelaturi rightly said, X-ray penetrate into the lattice planes inside the material. The structured orientation of the atoms inside the material results makes a material crystalline and so you see the pattern in the diffractogram.
To make it more simple, a sample of glass powder will look like irregular and crystalline under the SEM; but will just give you an amorphous hump in the XRD.@
Deepak Suthar XRD illustrates your crystallographic orientation with long range order, however, amorphous materials have short to medium range order that XRD show it as a hump peak. but in SEM if you have fully amorphous you will see only a clear surface with no crystalline area, no shape, but if you have pollycrystalline or some crystalls in your sample you will see it in SEM as a orriented morphology. it is better to performe SAD pattern and TEM to be sure it is fully amorphous. Also, try to performe SEM for different parts of your sample.
XRD uses X-Rays which penetrate into the material (few microns) and gives an idea of the crystallorgraphic orientation of the material, while the characteristic of amorphous material is they have a short/ medium range order and its detected as a hump shaped broad peak in the XRD diffractogram. SEM will generally show a clear surface if your material is fully amorphous while the presence of a polycrystalline features, is reflected in the form of highly oriented morphology. To further probe into the crystallographic aspect its better to perform SAED in TEM and that will give a clarity whether its fully amorphous or not, as TEM of amorphous material contains a hallow (white) and no diffraction rings. Kindly refer to the book on TEM by Prof. Barry Carter for a clarity on the science of TEM and SAED. Alternatively Raman spectroscopy can also be used for the same.