The invention discloses a method and system for metering and synchronously sampling high-voltage three-phase electric energy, and belongs to the field of high-voltage electric energy metering. The method comprises the steps of determining that a zero crossing point TA of a voltage AB phase of a high-voltage three-phase line is a sampling start point of a voltage A element of the high-voltage three-phase line and a zero crossing point TC of a voltage CB phase of the high-voltage three-phase line is a sampling start point of a voltage C element of the high-voltage three-phase line; determining that a reciprocal of a high-voltage three-phase voltage line frequency f is used as a sampling period T; and determining that data synchronous start point of the voltage A of the high-voltage three-phase line is TA and data synchronous start point of the voltage C of the high-voltage three-phase line is TC+T/6, and metering and synchronously sampling the high-voltage three-phase electric energy. Bythe method, the problem of synchronous sampling of a high-voltage three-phase electric energy metering device with a binary split structure is solved.