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In this letter, a route for synthesizing vertically aligned multi-walled carbon nanotubes (MWC-NTs) 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 800～900℃. The growth mechanism of the branched nanotubes was proposed and the possible reason that thiol enhanced branched nan-otubes 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.