Marine biological resource is one of the key components of ecological capital. Using the marine ecological capital assessment framework, the value of standing stock of biological resources was assessed in the Shandong provincial coastal waters in the western Yellow Sea. In 2006, the estimated biological resources in the total 31,584km² coastal waters of Shandong province was 1.02 million ton valuing 18.45 billion RMB. The biological resources of Shandong coastal waters include mainly fish, crustacean, cephalopod and jellyfish. Among those, fish contributed 71.4% of total value in 2006, where standing stock was 765.0 thousand ton, valued in 13.17 billion RMB. The standing stock of crustacean was 139.8 thousand ton, valuing 3.89 billion RMB, 21.1% of total value; the standing stock of cephalopod was 35.2 thousand ton, valued at 0.45 billion RMB and occupying 2.4% of total value. The standing stock of jelly fish was 64.6 thousand ton, valuing 0.94 billion RMB, 5.1% of total value. Among the seven coastal cities in Shandong province, the coastal waters of Weihai and Yantai cities had high levels of the standing stock value of biological resources, 32.7% and 27.9% respectively, of the total value. Qingdao, Rizhao and Weifang were at medium levels with 12.1%, 10.3% and 9.5% of total value respectively; Dongying and Binzhou cities were at low levels with 5.2% and 2.9% of total value respectively. In the coastal water of Shandong province, the spatial density of the standing stock value of biological resource was 584 thousand RMB/km². Among the seven coastal cities of Shandong province, Rizhao and Weifan cities were at the high level in the spatial density of standing stock value of biological resources, with 1.26 million RMB/km²; while Weihai and Binzhou cities was at medium levels with 868 and 866 thousand RMB/km²; Yantai and Qingdao were at low levels with 512 and 435 thousand RMB/km² respectively; Dongying city had even lower stock value of 113 thousand RMB/km². In the coastal waters of Shandong, each one hundred RMB of standing stock of biological resources support eight hundred RMB of ecosystem service output. The ratios of standing stock value to ecosystem service value in the coastal waters of the seven cities were 1 ∶ 4 for Binzhou, 1 ∶ 9 for Dongying, 1 ∶ 8 for Weifang, 1 ∶ 5 for Weihai, 1 ∶ 23 for Qingdao and 1 ∶ 6 for Rizhao. This study shows that there is strong linear correlation between the standing stock value of biological resources and these three services, including provisioning services, regulating service, and species biodiversity maintenance service in the coastal waters. These results suggest that these three services all rely on the standing stock of biological resources. More biological resources can support more provisioning and regulating services. The natural biological resources in Shandong coastal waters mainly include fish, crustacean, and cephalopod that directly contribute to fishing production. Moreover, the standing stock of biological resources and provisioning services (maricultural and fishing production, and oxygen production) both depend directly or indirectly on the primary production of phytoplankton and benthic algae through food chain interaction. The high relativity between the standing stock of biological resources and species diversity maintenance service indicates that the more biological resources can support more diverse species. The valuation of marine biological resources in this study would help government officials and the public to have a clear understanding on the benefits of these resources for human being. In turn, such understanding may help to improve the current utilization of coastal ecosystems and facilitate the ecosystem-based marine management at local scale.