Hi mahesh213,
Use the Replace method inside the FOR loop. Based on thr value check whether contains %, replace the Equal with Like operator.
I have updated your code. Change your code accordingly.
View
$scope.Save = function () {
    var Id1 = $scope.items;
    var rId = $scope.RName;
    var details = {};
    var array = [];
    for (var i = 0; i < $scope.items.length; i++) {
        var data = {};
        data.Text = $scope.items[i].CName;
        if ($scope.items[i].CType.toLowerCase() == 'dropdown') {
            data.Value = $scope.items[i].FromTable.toLowerCase() == "all" ? "%" : $scope.items[i].FromTable;
        } else if ($scope.items[i].CType.toLowerCase() == 'datepicker') {
            data.Value = ConvertDate($scope.items[i].Date.toString());
        } else if ($scope.items[i].CType.toLowerCase() == 'textbox') {
            data.Value = $scope.items[i].ValueCName;
        }
        array.push(data)
        details.RId = rId;
        details.details = array;
    }
    $http({
            method: "Post",
            url: "/Home/PopulateTable",
            dataType: 'json',
            headers: { "Content-Type": "application/json" },
            data: '{values: ' + JSON.stringify(details) + '}'
        }).success(function (data) {
            // Assign scope to bind gridview.
        }).error(function (err) {
    })
}
Controller
public JsonResult PopulateTable(Detail values)
{
    TestEntities db = new TestEntities();
    // Getting the query from Report1 table.
    string query = db.Report1.Where(x => x.RId == values.RId).Select(x => x.RQuery).FirstOrDefault();
    for (int i = 0; i < values.details.Count; i++)
    {
        string key = "{" + values.details[i].Text + "}";
        string value = "'" + values.details[i].Value + "'";
        // Replace the place holder with value.
        if (values.details[i].Value == "%")
        {
            query = query.Replace("= " + key, "LIKE '%'");
            query = query.Replace("=" + key, "LIKE '%'");
        }
        else
        {
            query = query.Replace(key, value);
        }
    }
    // Execute your final query and return json result and bind the gridview on success function.
    // Your code to return json.
    return Json(null, JsonRequestBehavior.AllowGet);
}