您可以使用sub，

sub("^([^_]*_[^_]*)_", "\\1-",df$a)

示例:

> a<-c("aa_bbb_cc_ddd","ee_fff_gg_hhh")
> b<-c("a","b")
> df<-data.frame(cbind(a,b))
> df
              a b
1 aa_bbb_cc_ddd a
2 ee_fff_gg_hhh b
> df$a <- sub("^([^_]*_[^_]*)_", "\\1-",df$a)
> df
              a b
1 aa_bbb-cc_ddd a
2 ee_fff-gg_hhh b