没有与您想要的线条相匹配的主题元素，因此您需要发挥创意。我更喜欢ggplot是独立的，所以与其在图上单独画线，我可能会把它们画成geom_path元素。这需要使用coord_cartesian并关闭裁剪和固定的y轴限制：

df %>% 
  ggplot(aes(x = epoca, y = n, fill = epoca)) +
  geom_col(width = 0.8, position = position_dodge(0.8)) +
  geom_text(aes(x = epoca, label = etiqueta),
            position = position_dodge(0.9), vjust = 0, size = 8) +
  ggh4x::facet_nested(cols = vars(ffvv, ano),
                      switch = "x",
                      scales = "free_x",
                      space = "free_x") +
  coord_cartesian(clip = "off", ylim = c(0, 3)) +
  geom_path(data = data.frame(epoca = rep("S", 6),
                              n = rep(c(-0.55, -0.15), 3),
                              ffvv = c("a", "a", rep("b", 4)),
                              ano = rep(c("2019", "2021", "2022"), each = 2)),
            position = position_nudge(x = -0.6)) +
  theme(strip.background = element_rect(fill = NA),
        strip.text = element_text(size = 25, lineheight = 0.6),
        strip.placement = "outside",
        axis.text.x = element_text(angle = 0, size = 27, 
                                   lineheight = unit(.8, "lines")))

另一个（手动）解决方案是使用{cowplot}：

library(cowplot)
ggdraw() + 
  draw_plot(g) +
  draw_line(x = c(0.42, 0.42),
            y = c(0.08, 0.21),
            lwd = 1.5,
            colour = "red")

其中g是您已经拥有的图，保存为变量。这不是一个完美的解决方案，因为它通常需要一点试错来获得正确的坐标。它使用了geom_path()，但这意味着你不必处理现有图的裁剪和坐标。

如果更多的是为了分离不同的方面，那么将colour = "red"添加到theme中的strip.background元素是一种替代方法：

另一种方法是使用geom_segment()：

library(tidyverse)

df %>% 
  ggplot(aes(x = epoca, y = n, fill = epoca)) +
  geom_col(width = 0.8, position = position_dodge(0.8)) +
  geom_text(aes(x = epoca, label = etiqueta),
            position = position_dodge(0.9), vjust = 0, size = 8) +
  ggh4x::facet_nested(cols = vars(ffvv, ano),
                      switch = "x",
                      scales = "free_x",
                      space = "free_x") +
  theme(strip.background = element_rect(fill = "white"),
        strip.text = element_text(size = 25, lineheight = 0.6),
        strip.placement = "outside",
        axis.text.x = element_text(angle = 0, size = 27, lineheight = unit(.8, "lines")))+
  theme(axis.title.x = element_text(margin=margin(50,0,0,0))) +
  coord_cartesian(clip = "off", ylim = c(0, 3)) +
  geom_segment(aes(x = 3, y = 0, xend = 3, yend = -0.5), color = "red")