To understand the mechanical properties of amorphous carbon (a-C)/boron nitride nanotube (BNNT) nanostructures, in situ mechanical tests are conducted inside a transmission electron microscope equipped with an integrated atomic force microscope system. The nanotube structure is modified with amorphous carbon deposited by controlled electron beam irradiation. We demonstrate multiple in situ tensile, compressive, and lap shear tests with a-C/BNNT hybrid nanostructures. The tensile strength of the a-C/BNNT hybrid nanostructure is 5.29 GPa with about 90 vol% of a-C. The tensile strength and strain of the end-to-end joint structure with a-C welding is 0.8 GPa and 5.2% whereas the lap shear strength of the side-by-side joint structure with a-C is 0.25 GPa.