Our national economic development imbalance leads to the different levels of regional marketization progress and government intervention.This paper analyses the effect of regional environment on regional innovation capability adopt Negative-binomial method in counting model based on the regional patent.It shows that the government has no distinct influence on improving total regional innovation capability,but has the active influence on the invention patent which improving capability of independent innovation and strengthening original science and technology exploitation capability.Regional market development has an important impact on regional innovation capability.The level of regional marketization is an important factor of regional innovation capability.Only improving regional marketization degree and governmental innovation guidance function is the key to enhance the regional innovation capability.