Я предполагаю, что вы хотите подвести итог больше, чем просто население городов для каждой страны:
>>> attributes = ['population', 'gdp', 'murders']
>>> x = {'usa': {'chicago': dict(zip(attributes, [10, 100, 1000])), 'nyc':dict(zip(attributes, [20, 200, 2000]))}, 'china': {'shanghai': dict(zip(attributes, [9, 90, 900])), 'nagasaki': dict(zip(attributes, [2, 20, 200]))}}
>>> x
{'china': {'shanghai': {'gdp': 90, 'murders': 900, 'population': 9}, 'nagasaki': {'gdp': 20, 'murders': 200, 'population': 2}}, 'usa': {'nyc': {'gdp': 200, 'murders': 2000, 'population': 20}, 'chicago': {'gdp': 100, 'murders': 1000, 'population': 10}}}
>>> for country, cities in x.iteritems():
y[country] = {attr:0 for attr in attributes}
for city, attributes in cities.iteritems():
for attribute, value in attributes.iteritems():
y[country][attribute] += value
>>> y
{'china': {'gdp': 110, 'murders': 1100, 'population': 11}, 'usa': {'gdp': 300, 'murders': 3000, 'population': 30}}