The invention relates to the technical field of information, in particular to a block chain-based carbon emission permit and green certificate combined transaction system, which comprises an access subsystem, a filling subsystem, a matching subsystem and a settlement subsystem, and is characterized in that an enterprise transfers a carbon emission permit and / or a green certificate into the access subsystem, transfers a corresponding number of certificates into an enterprise virtual account, and checks the corresponding number of certificates; the filling subsystem receives a purchase filling order and a sale filling order of an enterprise, the filling subsystem extracts hash values of the purchase filling order and the sale filling order and uploads the hash values to a block chain for storage, the matching subsystem generates a lineation unit price, so that the number of transaction certificates under the lineation unit price is maximum, and the settlement subsystem performs fund settlement according to the transaction purchase filling order and the sale filling order. And the corresponding token is transferred to the virtual account of the corresponding transaction purchasing enterprise, and the enterprise exchanges the token into carbon emission permissions or green certificates with the consistent number through the access subsystem. The method has the substantive effects that the trading volume can be effectively improved, and the loss caused by the fact that an enterprise cannot accurately grasp the market law is reduced.