Lateral connectivity between a main channel and a former channel plays an integral role in maintaining ecological functions of stream-floodplain ecosystems. This study virtually restored the connectivity of the former channel, which is currently isolated by channelization, in the Mangyeong River, Korea. Fish habitat improvement after the connectivity restoration was evaluated using River2D, two-dimensional depth-averaged hydraulic modeling, depending on normal and flood flow conditions. Target fish species were crucian carp (Carassius auratus), which are known as lentic species, and pale chub (Zacco platypus), known as lotic species. The weighted usable area (WUA) of the two species was increased after the connectivity restoration: the two-way connection between the main and formal channels was more effective than the one-way connection. The result of the physical habitat simulation at a flood flow condition demonstrated an increased rate of the WUA than during a normal flow condition. In particular, the WUA of pale chub increased about four times on the two-way connectivity restoration. This result suggests that habitat availability of both lentic and lotic fish species will increase after a connectivity restoration, and a two-way connectivity restoration may be more effective. In addition, the restored formal channel would function as a shelter for fish during the flood season.