Creating nested JSON using PHP MySQL

To efficiently group the subarray data, you should implement temporary keys. cityId is a suitable value to group by -- because cityNames may intentionally duplicate in the future but cityId must never un/intentionally duplicate in your database table.

When each new cityId is encountered, the conditional isset() call will determine whether a new/full set of data should be stored, or if data should merely be appended to the subarray.

I am calling array_slice() since it cuts down on unnecessary syntax / code-bloat.

After iterating through all of the rows, you can reindex the $result array, nest it inside runBasedOnCity, and add the status element.

I'll show my demo with PRETTY_PRINT so that it is easier to read, but in your actual code, you should remove the parameter. Also, a word of advice -- try to keep your variable names brief for improved readability.

Code: (Demo)

$resultset = [    ["id" => "1", "cityId" => "1", "cityName" => "Bengaluru", "runId" => "2", "distance" => "10k", "status" => "1"],    ["id" => "2", "cityId" => "1", "cityName" => "Bengaluru", "runId" => "1", "distance" => "5k", "status" => "1"],    ["id" => "3", "cityId" => "1", "cityName" => "Bengaluru", "runId" => "5", "distance" => "3k", "status" => "0"],    ["id" => "4", "cityId" => "2", "cityName" => "Chennai", "runId" => "1", "distance" => "5k", "status" => "1"],    ["id" => "5", "cityId" => "2", "cityName" => "Chennai", "runId" => "2", "distance" => "10k", "status" => "1"],    ["id" => "6", "cityId" => "2", "cityName" => "Chennai", "runId" => "4", "distance" => "15k", "status" => "1"]];foreach ($resultset as $row) {    if (!isset($result[$row["cityId"]])) {        $result[$row["cityId"]] = array("id" => $row["id"], "cityId" => $row["cityId"], $row["cityName"] => array(array_slice($row,-3)));    } else {        $result[$row['cityId']][$row["cityName"]][] = array_slice($row,-3);    }}if (!isset($result)) {   // don't need to check rowCount() at all    $result = 'Runs not found';} else {    $result = array_values($result);}$result = array("status" => true, "runsBasedOnCity" => $result);var_export(json_encode($result, JSON_PRETTY_PRINT));

Output:

'{    "status": true,    "runsBasedOnCity": [        {            "id": "1",            "cityId": "1",            "Bengaluru": [                {                    "runId": "2",                    "distance": "10k",                    "status": "1"                },                {                    "runId": "1",                    "distance": "5k",                    "status": "1"                },                {                    "runId": "5",                    "distance": "3k",                    "status": "0"                }            ]        },        {            "id": "4",            "cityId": "2",            "Chennai": [                {                    "runId": "1",                    "distance": "5k",                    "status": "1"                },                {                    "runId": "2",                    "distance": "10k",                    "status": "1"                },                {                    "runId": "4",                    "distance": "15k",                    "status": "1"                }            ]        }    ]}'

After explaining how you wanted to preserve the id values in the subarrays, here is that solution:

Code: (Demo)

foreach ($resultset as $row) {    if (!isset($result[$row["cityId"]])) {        $result[$row["cityId"]] = array("cityId" => $row["cityId"], $row["cityName"] => array(array("id" => $row["id"])+array_slice($row,-3)));    } else {        $result[$row['cityId']][$row["cityName"]][] = array("id" => $row["id"])+array_slice($row,-3);    }}if (!isset($result)) {   // don't need to check rowCount() at all    $result = 'Runs not found';} else {    $result = array_values($result);}$result = array("status" => true, "runsBasedOnCity" => $result);var_export(json_encode($result, JSON_PRETTY_PRINT));