To know the basic configuration and application characteristics of aluminum (Al) nanostructure, the structure performances of carbon nanotube (CNT) and boron-nitride NT (BNNT) filled with Al atoms are studied through molecular dynamics. Optimization results show that the Al atoms in the tube are arranged neatly into various shapes of nanowires. A bunch of one-dimensional (1D) Al nanowires (AlNWs) is formed in (5, 5) CNT and BNNT, and large beams of AlNWs are formed in (10, 10) NT, including 11 beams of 1D AlNWs with highly axial symmetry in (10, 10) CNT and 5 beams of spiral AlNWs in BNNT (10, 10). Further data analysis for radical distribution function (RDF) shows that AlNWs inside CNT have larger atomic distribution density, but those inside BNNT with larger diameter have better crystallinity than those with similar size inside the CNT. These results can provide a method of designing the nanowires with different structures and shapes in different micro-nano devices (such as nanospring, nanosolenoid, and others). Comparison of the axial compression behaviors of the composite NTs and their energy analysis reveal that the critical buckling strain of AlNW@CNT is significantly larger than that of AlNW@BNNT. For the same type of compound structure, the buckling strain decreases with NT diameter increasing. Therefore, smaller AlNW@CNT has stronger axial compressive resistance. The main reasons are as follows: 1) The AlNW in carbon NTs has a relatively large Al atomic distribution in the axial direction, which is conducive to the formation of σ bond to increase structural stability and mechanical performance. It also plays a decisive role in enhancing compressive performance. 2) The AlNW in the large-diameter boron nitride NTs is helical in shape, and more Al atoms are distributed in the direction of the cross section, thereby relatively reducing the number of axial pressure-bearing atoms. In addition, for the same type of nanotube, a tube with a small diameter results in closer hexagons to the tube wall and larger interaction. These conditions are more conducive to resisting the transverse subsidence under axial pressure. The energy analysis results indicate that the van der Waals force is one of the main causes for NT composite stability and increasing compressive strength. These results can provide a reference for selecting different Al nanowire-reinforced composite structures under different application conditions, such as high temperature, high pressure, oxidation resistance, and others.