A control method and system of neutral section passing of multi-locomotive short broke trains. Distance traveled by a train after a primary multiple unit enters a neutral section is calculated in real time, so that a neutral section passing procedure of a secondary multiple unit is effectively controlled, thereby solving the problem that when the multi-locomotive short broke trains operate with double-raised pantographs, if the distance between the two pantographs is shorter than the length of a neutral zone of a neutral section and longer than the length of a no-electricity zone of the neutral section, when the two pantographs pass through the neutral sections, the two pantographs will span the two neutral sections and generate an interphase short circuit. The method improves safety of the EMU when it passing neutral section and ensure that the EMU can reliably pass through the neutral section with double-raised pantographs. The present invention has the advantages of being safe, reliable, easy to implement and convenient to promote and apply.