Finally i have found the solution to update the twin-module desired properties ,
DeviceTwinDevice constructor can be used with a deviceId and moduleId, so example below:
DeviceTwin twinClient = DeviceTwin.createFromConnectionString(connectionString);
DeviceTwinDevice twin = new DeviceTwinDevice(deviceId,moduleId);
twinClient.getTwin(twin);
//Get the module desired properties
Set<com.microsoft.azure.sdk.iot.service.devicetwin.Pair> properties = twin.getDesiredProperties();
//..
//Logic to modify the properties
//..
//Set the desired properties
twin.setDesiredProperties(properties);
//Update the twin module with the new desired properties
twinClient.updateTwin(twin);