OK for example the numeric value of one of my data is large and the numeric value of one of my data is small. 

A = [130000 310000 200000 400000]'; B = [16 32 5 10]';

I am doing the following. 

figure; bar(1:4,[A B],0.5,'stack');

Since the value of A is lot high than B, I want a secondary y-axis. Otherwise the values of B cannot be seen on the stacked bar chart. 

Answer: 

You can use plotyy to plot two bar charts on different y-axes in the same figure. 

x = [1,2,3]; y1 = [1000,2000,3000]; y2 = [0.5,0.3,0.1]; [AX,H1,H2] = plotyy(x, y1, x, y2, 'bar', 'bar'); set(H1, 'FaceColor', [1 0 0], 'BarWidth', 1)

This isn't a stacked bar chart like you had before (one set of data vertically on top of the other) but it doesn't make sense include data on different scales in a stacked bar chart.