I been using stool softener for my 3 month baby since she was 2 month old. When can I slowly take her off of that? Will this mess her digestive system

Anytime/no. Babies are a growing system and all the worry about becoming dependent on stool softeners or wetting agents do not apply. Older adults, maybe, but infants and children, no. If the kid needs this on and off for the first years of life, please use it. Recurrent constipation is common in kids and most often results from parents quit after early results and don't treat long enough to solve the problem.