Superconducting qubits based on Al/AlOx/Al Josephson junction are one of the most promising candidates for the physical implementation of universal quantum computers. Due to scalabilityand compatibility with the state-of-the-art nanoelectronic processes one can fabricate hundreds of qubits on a single silicon chip. However, decoherence in these systems caused by two-level-systems in amorphous dielectrics, including a tunneling barrier AlOx, is one of the major problems. We report on a Josephson junction thermal annealing process development to crystallize an amorphous barrier oxide (AlOx). The dependences of the thermal annealing parameters on the room temperature resistance are obtained. The developed method allows not only to increase the Josephson junction resistance by 175%, but also to decrease by 60% with precisions of 10% in Rn. Finally, theoretical assumptions about the structure modification in tunnel barrier are proposed. The suggested thermal annealing approach can be used to form a stable and reproducible tunneling barriers and scalable frequency trimming for a widely used fixed-frequency transmon qubits.