The limits (and Y ticks) are automatically calculated by the PLOTYY function, so that they are aligned for both sets of data. However, you can modify them by changing the axes' YLim values.
x = 1:10;
y1 = sin(x);
y2 = 10*cos(x);
[ax,h1,h2] = plotyy(x,y1,x,y2);
set(ax(1),'YLim',[-2 2])
set(ax(2),'YLim',[-15 15])
However, now that the Y limits are changed, you may want to change some other properties of the axes that affect its appearance. One option is to set the Box property for the first axes to 'off', to avoid extra ticks on the right side. The extra ticks that appear were previously aligned with the ticks from the second axes. Try the following code:
set(ax(1),'Box','off')
To change the locations of the Y tick marks as well:
set(ax(1),'YTick',[-2:.5:2])
set(ax(2),'YTick',[-15:5:15])
