The boron-substituted MCM-41 was hydrothermally synthesized using Na2B4O7 and H3BO3 as boron sources. The influence of the nature of the boron source on the textural properties as well as the stability of MCM-41 structure and the state of boron upon different procedures such as NH3 treatment, ion-exchange, and calcination were investigated using XRD, FTIR, TEM, and B-11 MAS-NMR techniques. Na2B4O7 has proven its ability to improve uniform long-range ordering compared to the pure silica MCM-41 analogue. The order of the uniform hexagonal mesopores in the MCM-41 products obtained following the same synthesis conditions is B-MCM-41 prepared from Na2B4O7 > B-MCM-41 prepared from H3BO3 > pure silica MCM-41. The counterbalancing cations such as Na+ and NH4+ were found to be operative in stabilizing tetrahedral boron while H+ induces unstability. The ion-exchange procedures were found to be accompanied by a partial collapse of B-MCM-41 structure. The nature of counterbalancing cations was also found to play a role in deciding the state of boron and its stability during hydration/dehydration process.