A total of 88 marine protected areas (MPAs) have been set up in the Shandong coastal waters in the western Yellow Sea. These 88 marine protected areas include 12 natural reserves, 30 special protected areas, and 46 aquatic germplasm resources protection areas. Based on the contingent valuation method (CVM), a questionnaire was developed to survey the willingness to pay (WTP) to maintain all 88 MPAs. The survey samples were taken from Jinan (as an example of inland cities) and Qingdao (as an example of coastal cities) in November 2014. The results suggested that the WTP of the urban residents in Shandong province represents the costs that people are willing to pay for keeping the ecosystem diversity from all Shandong MPAs. The average WTP among inland residents was 102.15 CNY per person, which is 23.05 CNY higher than that of coastal residents (82.29 CNY per person). Based on the 2014 survey, the total value of ecosystem diversity maintenance of the 88 MPAs was 4.37 billion CNY, with an average of 49.7 million CNY per MPA. Furthermore, this value per MPA ranged from 17.5 to 274 million CNY per MPA. For the 12 natural reserves together, the value was 1.6 billion CNY, with an average of 135 million CNY per MPA, and it ranged from 73 to 274 million CNY per MPA. For the 30 special protected areas, the value of ecosystem diversity maintenance was 1.45 billion CNY, the average was 48.9 million CNY per MPA, and the values per MPA ranged from 36 to 127 million CNY per MPA. Finally, for the 46 aquatic germplasm resources protection areas the total ecosystem diversity maintenance value was 1.29 billion CNY, the average was 28 million CNY per MPA, and it ranged from 17.5 to 97 million CNY per MPA. Furthermore, the spatial average of ecosystem diversity maintenance value for the 88 MPAs was 4.49 million CNY/km², ranging from 54.4 thousand to 173 million CNY/km². The spatial value of the 12 natural reserves was 18.25 million CNY/km², for the 30 special protected areas it was 2.69 million CNY/km², and for the aquatic germplasm resources protection areas it was 2.07 million CNY/km². The value of the natural reserves established by the environmental protection department was higher than for the special protected areas established by the marine management department. In addition, the value of the aquatic germplasm resources protection areas established by the fisheries management department was the lowest. Our study suggests that the value of ecosystem diversity maintenance should be covered in the selection criteria and management objectives of MPAs. Habitats with the highest value of ecosystem diversity maintenance should be set up as natural reserves that have the strictest management measures. Their management objectives should include increasing or keeping the ecosystem diversity maintenance value. The areas with a lower value should be set up as special protected areas or aquatic germplasm resources protection areas. These should have stricter management measures, and their management objective should include maintaining the value of ecosystem diversity maintenance.