In this letter, a route for synthesizing vertically aligned multi-walled carbon nanotubes(MWCNTs) with branched nanotubes in large area was reported. The branched MWCNTs up to about 30% can be generated by the pyrolysis of iron(Ⅱ) phthalocyanine in presence of thiol under Ar/H2 at 800900℃. The growth mechanism of the branched nanotubes was proposed and the possible reason that thiol enhanced branched nanotubes growth is discussed. The as-prepared samples provide a suitable candidate to investigate the special electrical or thermal properties of CNTs with branched structures further.