This paper investigated spatial structures of 3418 national protected areas (NPAs) grouped into 13 types using GIS and quantitative analysis, including point patterns, Ripley’s K function, hotspot clustering, quadrat analysis, and Gini coefficient. Spatial accessibility was calculated for all NPAs from matrix raster data using cost weighted distance on the ArcGIS platform. The results are as follows: (1) The NNI of NPAs is 0.515, Gini is 0.073, all of which indicates distribution was shown to be a spatially dependent agglomeration, and more balanced in the provinces. The national key parks and the national water conservancy scenic spots had present the strongest aggregation, with NNI of 0.563 and 0.561 respectively, and K index indicates reducing aggregation when distance exceeds 600 km. (2) The national forest parks account for the largest proportion of 22.87% of all NPAs, and the world biosphere reserves the least of 0.77%. The number of NPAs in Shandong with 240 had been the largest one in all the provinces, while Tianjin had the least number including 9 NPAs. (3) There is only one hot spot in the first-class zone, 5 in the second-class zones, and 51 in the third-class zones, which indicates NPAs are also aggregated at microscopic scales. (4) The hotspot NPA regions were mainly concentrated in the middle and lower reaches of the Yellow and Yangtze rivers, east of 100°E. High density of NPAs were generally in flat, water-rich, broad-leaved forest dominated plains and low mountain areas, with fertile soil, pleasant weather, long cultural history, and high transportation accessibility. (5) Average NPA accessible time is 60.05 min, with 70.76% regions being within 60 min, and the furthest was 777 min. The distribution of accessibility was positively related to the traffic lines. Interdepartmental protectionism has meant the various departments developed different management systems, standards, and technical specifications.