In the case of islanding from the distribution network, problems such as source-load power loss under multi-zone island isolation will challenge the autonomous operation of multi-microgrids with three-phase/single-phase hybrid structure. In order to make full use of the resources in the multi-microgrids to realize the reliable and efficient operation of the system as a whole, this paper proposes a multi-time scale regional autonomous control strategy for multi-microgrids with three-phase/single-phase hybrid structure. The dynamic update islanding combination is controlled by the hourly dynamic island combination and the simultaneous search switching to achieve the overall resource allocation optimization. The source-storage-load power and state redistribution are dynamically realized through minute-level centralized coordination and optimization, so that the constraints of the three-phase unbalance are met and the source-load shedding are minimized. The power fluctuations of the sources and loads within each sub-microgrid are suppressed by using the second-level off-grid real-time power control. Moreover, the tie-line power can be maintained as the original given value and the three-phase unbalance degree index can be achieved. The multi-microgrids model with three-phase/single-phase hybrid structure based on DIgSILENT platform is used to verify the correctness and effectiveness of the proposed strategy.