Can I claim the child tax credit without affecting my non-EU wife's visa extension?

I'm British citizen and my wife is non-European. She has spouse visa which will expire by 29 June 2020. After that she can apply for indefinite leave to remain. At the moment we both work fulltime and each of us earns £20000/year. Now we have 02 children and both of them are going to Nursery fulltime in this October 2019. So we are looking at the child tax credit allowance which is now replaced by Universal credit. We would like to apply for this child tax credit to help us cover abit of the child care cost. But my concern is that if this will affect to my wife's visa? She will need to renew it next June 2020.

Can you please advise if I can apply for this child tax credit on my own? Will it affect to my wife's visa? Or can we both apply together and it wont affect to her visa? Please help.

Many thanks.