Мой косяк оказался. Я одну точку забыл.
import numpy as np
from scipy.interpolate import griddata
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
x_list = np.array([54.0, 54.0, 54.0, 24.0, 24.0, 24.0, 24.0, 0.0, 0.0, 0.0])
y_list = np.array([40.0, 20.0, 0.0, 0.0, 40.0, 20.0, 0.0, 40.0, 20.0, 0.0])
z_list = np.array([105.4, 104.5, 103.65, 103.65, 105.45, 104.7, 103.95, 105.5, 104.85, 104.25])
xi = np.linspace(min(x_list), max(x_list))
yi = np.linspace(min(y_list), max(y_list))
grid_x, grid_y = np.meshgrid(xi, yi)
grid_z1 = griddata((x_list, y_list), z_list, (grid_x, grid_y), method='nearest')
grid_z2 = griddata((x_list, y_list), z_list, (grid_x, grid_y), method='linear')
grid_z3 = griddata((x_list, y_list), z_list, (grid_x, grid_y), method='cubic')
print grid_z2
##z1 = grid_z2 = griddata((x_list, y_list), z_list, (grid_x, grid_y), method='linear')
fig = plt.figure()
ax1 = fig.add_subplot(221, projection='3d')
surf = ax1.plot_surface(grid_x, grid_y, grid_z1)
ax2 = fig.add_subplot(222, projection='3d')
surf = ax2.plot_surface(grid_x, grid_y, grid_z2)
ax3 = fig.add_subplot(223, projection='3d')
surf = ax3.plot_surface(grid_x, grid_y, grid_z3)
plt.show()