For renewable energy driven off-grid hydrogen generation systems, the intermittent and instability nature significantly hinders the electrolyzers' service life and operation safety. Here a variable-periodsequence control strategy is developed for an off-grid photovoltaic-PEM electrolyzer hydrogen generation system via multi-layer DC-DC converters, which control power allocation for the PEM electrolyzer according to the accumulated operation durations under different operation states. The dynamic performance under the fixed and variable period sequence control strategies are systematically investigated. Under the fixed period sequence control strategy, less electrolyzer number contributes to deducing standard deviations of rated/fluctuating power operation durations. Under the variable period sequence control strategies, the standard deviations of the operation duration under the rated and fluctuating power state both are much smaller than those under the fixed period sequence control strategy. When longer sequence period employed at higher solar radiation intensity, the minimum standard deviations of the operation duration under the rated and fluctuating power states are decreased by 28.0% and 44.8%, respectively. When longer sequence period employed at lower solar radiation intensity, the minimum standard deviations are decreased by 49.7% and 51.3%, respectively. The variable sequence control strategy can better allocate electrolyzers’ operation states and improve the system operation conditions.