I am trying to display a list of points on the map. but these latitude and longitude are given as decimals:
      index    X              y 
      1    24050.0000    123783.3333
      2    24216.6667    123933.3333
      3    24233.3333    123950.0000
      4    24233.3333    124016.6667 
         ........................
These data is taken from sources(page). It seems I can use these data directly with Google Map API, so what should I do?
How can I convert them into a format compatible with Google Map API to display? I am using JavaScript.
                        
Looks to me those points are just the WGS84 coordinates multiplied by 1000. The code below gives me a reasonable location in Japan, where data is the array of points in the file you reference.
});
proof of concept fiddle