Adding figsize=(w,h)to the first line should do the trick. What do you mean by "it has no effect"?
For instance:
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
fig1=plt.figure(figsize=(8,5))
ax11=fig1.add_subplot(211,projection='3d')
ax12=fig1.add_subplot(212)
fig1.get_size_inches()
fig2=plt.figure(figsize=(4,4))
ax21=fig1.add_subplot(211,projection='3d')
ax22=fig1.add_subplot(212)
fig2.get_size_inches()
fig1.savefig('fig1.png',dpi=300)
fig2.savefig('fig2.png',dpi=300)
png 300dpi:
$ identify fig1.png
>>> fig1.png PNG 2400x1500 2400x1500+0+0 8-bit sRGB 118KB 0.000u 0:00.000
$ identify fig2.png
>>> fig2.png PNG 1200x1200 1200x1200+0+0 8-bit sRGB 86.9KB 0.000u 0:00.000