This has been a problem as long as I can remember. There is a File Exchange contribution, Tools for Axis Label Alignment in 3D Plot (link) that apparently does this automatically.
Another option is just to experiment with the 'Rotation' property until it works. Note that if you rotate the axes, you have to re-code the 'Rotation' angle values.
Example —
colormap(hsv);
s = 0:0.025:3;
t = s;
[x,y] = meshgrid(s,t);
z = x.^2 - y.^2;
mesh(x,y,z);
xlabel('time[sec]', 'Rotation',20)
ylabel('position[mm]', 'Rotation',-30)
zlabel('force[N]')