I'd set the limits of each axis individually, something like this:
% some data:
t = 1:12;
T = 20*sin(pi*t/12);
P = 30*sin(pi*t/12)+5*randn(size(t))+30;
% Plot the data
[ax,h1,h2] = plotyy(t,T,t,P);
% Set the axis limits of the T data:
set(ax(1),'xlim',[1 12],...
'ylim',[0 50],...
'ytick',0:10:50,...
'ycolor','r')
% Set the color of the T data line:
set(h1,'color','r','linewidth',2)
% Set the P data color and axis limits:
set(ax(2),'xlim',[1 12],...
'ylim',[0 100],...
'ytick',0:20:100,...
'ycolor','b')
set(h2,'color','b','linewidth',2)
box off
