Deserializing with a json file with inner classes with JSON.NET C#

Whenever you have a JSON property that might be duplicated, it will be easiest to represent the value of that property as JSON array, rather than multiple properties with duplicated names. I.e. instead of

{
    "EXE" : {"id":1},
    "RPC" : {"name":"a"},        
    "EXE" : {"id":2},
}

You want to do:

{
    "EXE" : [{"id":1}, {"id":2}],
    "RPC" : [{"name":"a"}]        
}

Similarly, in the VM class, name appears multiple times, so name should be an array as well:

public class VM
{
    public string [] name { get; set; }
    public string args { get; set; }
}

(It's not impossible to deserialize duplicated property names, just difficult, and requires a custom converter. See How to deserialize JSON with duplicate property names in the same object. Since you control your JSON format, I'd recommend avoiding this. Using a nested object with indexed properties as you propose in your question is also an option; it is less difficult but still requires custom conversion. See How to parse this JSON using Newton Soft for nested object. But using a JSON array is easiest.)

Next, you need to tell Json.NET how to map c# property names to JSON property names when they are inconsistent. For instance, in your JSON you have a property "EXE" but in c# the property name is public EXE[] exeList { get; set; }. You can either rename the JSON properties, rename the c# properties, or make the mapping using [JsonProperty]:

public class UplinkPage
{
    [JsonProperty("VM")]
    public VM[] vmList { get; set; }

    [JsonProperty("EXE")]
    public EXE[] exeList { get; set; }

    [JsonProperty("RPC")]
    public RPC[] rpcList { get; set; }

    [JsonProperty("JAR")]
    public JAR[] jarList { get; set; }

    [JsonProperty("link")]
    public Link[] linkList { get; set; }
}

I notice also that your EXE object sometimes has a "data-prog" property, and sometimes just a "prog". You should standardize on one.

Thus your JSON should look like:

{
  "missionName": "missionname",
  "thumb_image": "pics/mission-info.png",
  "uplinkPage": [
    {
      "RPC": [
        {
          "name": "RPC",
          "rpc": "",
          "args": ""
        }
      ],
      "EXE": [
        {
          "name": "app1",
          "prog": "prog1",
          "args": "args1"
        },
        {
          "name": "app2",
          "prog": "prog2",
          "args": "args2"
        }
      ],
      "VM": [
        {
          "name": [
            "VM",
            ""
          ],
          "args": ""
        }
      ],
      "JAR": [
        {
          "name": "JAR",
          "prog": "",
          "args": ""
        }
      ],
      "link": [
        {
          "name": "somelink",
          "url": ""
        }
      ]
    }
  ]
}

And your classes should look like:

public class EXE
{
    public string name { get; set; }
    public string prog { get; set; }
    public string args { get; set; }
}

public class RPC
{
    public string name { get; set; }
    public string rpc { get; set; }
    public string args { get; set; }
}

public class VM
{
    public string [] name { get; set; }
    public string args { get; set; }
}

public class JAR
{
    public string name { get; set; }
    public string prog { get; set; }
    public string args { get; set; }
}

public class Link
{
    public string name { get; set; }
    public string url { get; set; }
}

public class UplinkPage
{
    [JsonProperty("VM")]
    public VM[] vmList { get; set; }

    [JsonProperty("EXE")]
    public EXE[] exeList { get; set; }

    [JsonProperty("RPC")]
    public RPC[] rpcList { get; set; }

    [JsonProperty("JAR")]
    public JAR[] jarList { get; set; }

    [JsonProperty("link")]
    public Link[] linkList { get; set; }
}

public class Rootobject
{
    public string missionName { get; set; }
    public string thumb_image { get; set; }
    public UplinkPage[] uplinkPage { get; set; }
}

prototype fiddle.