Ensilage is a traditional technology for green fodder crops storage, which is gradually used in the storage of raw materials for biogas production. The energy crop of giant reed harvested at two different times was used as material for ensilage and conducted for a period of 90 days. Changes in chemical composition and subsequent methane production of ensiled giant reed by anaerobic digestion were examined. The results showed that the difference in water soluble carbohydrate (WSC) content of giant reed caused by harvest time was the main reason for the difference in performance of giant reed ensilage. The WSC content was 2.80% of dry matter (DM) for the giant reed of early harvest (end of August). There was no accumulation of lactic acid during ensilage of early-harvested giant reed, and also urea addition reduced the DM by 280% and significantly enhanced by 101.3% of lignin degradation during the whole ensilage. The WSC content achieved 4.94% DM for the giant reed of late harvest (early October), and the DM loss was about 1% during 90 days’ ensilage. The cumulative production of lactic acid was increased by 237.5%, and the lignin degradation was increased by 43.8% for late-harvested giant reed via urea-assisted ensilage. Compared with non-ensiled giant reed, the cumulative methane production of early-harvested and late-harvested giant reed via 90 days’ urea-assisted ensilage were increased by 25.6% and 17.4% during anaerobic digestion, respectively. Therefore, early harvest led to a low content of WSC and an undesirably ensilage, whereas urea-assisted treatment can effectively reduce the ensiled DM loss and improve the subsequent methane production of giant reed.