Investigations of crystal habit, quality and defects analysis of natural diamond and HPHT synthetic diamonds from Fe-C(H) and Ni-C system by Raman and PL spectra indicate that most of the diamonds from Fe-C(H)system have an octahedral habit which is the main habit in natural diamond, while most of the diamonds from Ni-C system have a hexakisoctahedral habit. Because there are more photoluminescence centers in synthetic diamond from Ni-C system than that from Fe-C(H)system, and in synthetic diamond than in natural diamond, the quality of natural diamond is best though it forms in more polygenic environment, which suggested that during the process of diamond formation clearing“impurity”must occur. Therefore, the authors believe that not only the substance system variance but also time and space conditions for diamond formation should be considered when the authors try to probe into the relations of formation process between natural and HPHT synthetic diamonds.