You are actually asking two nested questions.
Hold on applies:
data = rand(100,3);
boxplot(data)
hold on
line(1:3,[1,1,1])
To add a line on a different Y range:
data = rand(100,3);
boxplot(data)
set(gca,'box','off')
% Remove all other objects except the axes
h = copyobj(gca,gcf);
delete(allchild(h))
% Some features (you have to tweak the Y range manually)
set(h,'Color','none','XtickL','','YAxisLoc','right',...
'next','add','Ylim',[200,300])
% Add a line
plot(h,1:3,[220,240,260])
