The invention discloses a method and a system for recovering regenerative brake energy of an energy storage type urban rail based on a supercapacitor. The method comprises the following steps of connecting a direct current traction network of the urban rail through a chopping unit and a supercapacitor unit, wherein the chopping unit comprises two bidirectional chopping module units; according to the connecting type of the two bidirectional chopping module units of the direct current traction network, and the voltages of the direct current network and the supercapacitor, controlling the charging and discharging of the supercapacitor unit. The system comprises the chopping unit, the supercapacitor unit, a chopping control module and a direct current isolation switch unit, wherein the chopping unit comprises the two bidirectional chopping module units which are connected in series or parallel, and each bidirectional chopping module unit comprise one or more than one bidirectional DC / DC (direct current / direct current) chopping module which is connected in parallel. The method and the system have the advantages that the regenerative brake energy of the urban rail can be recovered and fed back, and the method and the system can be applied to the common DC1500V / DC750V direct current traction networks; the universality is strong, the reliability is high, the stability is good, the production cost is low, and the flexibility is high.