The correct punctuation is either He does well in English although he prefers math to English (no comma at all) or He does well in English, although he prefers math to English (comma between the independent clause and the dependent clause but still no comma after although. (This is an example of an instance in which we have an option whether to set off the closing dependent clause with a comma. If we want to give a little more emphasis to the contrast expressed by the although clause, we may opt for using the comma.)