I couldn't understand the control strategy involved in charging the battary. I am using H2 storage + battaries.

In a system that includes both a battery bank and a hydrogen storage tank, HOMER assumes that charging the battery bank always takes precedence over filling the hydrogen tank.  That's because the round-trip efficiency for a hydrogen storage system is typically less than 50%, which is much lower than the 70%-85% you can expect from a battery bank.  So HOMER won't put electricity towards the electrolyzer to fill the hydrogen tank unless the battery bank is completely charged.