Boron nitride nanotubes (BNNTs) have many fascinating properties and a wide range of applications. An improved ball milling method has been developed for high-yield BNNT synthesis, in which metal nitrate, such as Fe(NO3)3, and amorphous boron powder are milled together to prepare a more effective precursor. The heating of the precursor in nitrogen-containing gas produces a high density of BNNTs with controlled structures. The chemical bonding and structure of the synthesized BNNTs are precisely probed by near-edge X-ray absorption fine structure spectroscopy. The higher efficiency of the precursor containing milling-activated catalyst is revealed by thermogravimetric analyses. Detailed X-ray diffraction and X-ray photoelectron spectroscopy investigations disclose that during ball milling the Fe(NO3)3 decomposes to Fe which greatly accelerates the nitriding reaction and therefore increases the yield of BNNTs. This improved synthesis method brings the large-scale production and application of BNNTs one step closer.