I'm 11 weeks pregnant, my doctor advice me to take metronidazole 500mg 2x aday for my bacteria vaginosis, is it safe for my baby?

Risk/benefit. While most medications cannot be absolutely guaranteed "safe", many medications are considered at low risk and the benefit of treating the underlying disorder is considered beneficial enough to justify a theoretical risk. This is the case with the standard treatment for BV that you described.
Yes. This is definitely a safe regimen for treatment in pregnancy. You can check the cdcs website regarding bacterial vaginosis and pregnancy and they will confirm that this is an appropriate treatment.