This will work if both datasets ( x1 and y1) have the same length:
data = rand(10,2);
x1 = data(:,1);
y1 = data(:,2);
h1 = qqplot(x1);
hold on;
h2 = qqplot(y1);
xData_x1 = get(h1(1),'Xdata');
yData_x1 = get(h1(1),'YData');
xData_y1 = get(h2(1),'Xdata');
yData_y1 = get(h2(1),'YData');
tempVal = max([yData_x1;yData_y1]);
yData_y1 = min([yData_x1;yData_y1]);
yData_x1 = tempVal;
patch([xData_x1 , fliplr(xData_x1)],[yData_x1 , fliplr(yData_y1)],'blue','FaceAlpha',0.5)
