您可以使用group\ U concat using group by

SELECT r.id as rid
    , r.entrada as rentrada
    , r.salida as rsalida
    , c.nombre as cnombre
    , c.telefono as ctelefono
    , c.dni as cdni
    , c.apellidos as capellido
    , group_concat(e.id_cliente)
  FROM reserva r 
  INNER JOIN cliente c on r.id_mainclient = c.id 
  INNER JOIN estancia e on r.id = e.id_reserva
  GROUP BY r.id
  ORDER BY rid DESC

或使用适当的分隔符和顺序

SELECT r.id as rid
, r.entrada as rentrada
, r.salida as rsalida
, c.nombre as cnombre
, c.telefono as ctelefono
, c.dni as cdni
, c.apellidos as capellido
, group_concat(e.id_cliente ORDER BY e.id_cliente ASC SEPARATOR ' ')
FROM reserva r 
INNER JOIN cliente c on r.id_mainclient = c.id 
INNER JOIN estancia e on r.id = e.id_reserva
GROUP BY r.id
ORDER BY rid DESC

或者如果你还需要c.dni

SELECT r.id as rid
    , r.entrada as rentrada
    , r.salida as rsalida
    , c.nombre as cnombre
    , c.telefono as ctelefono
    , c.dni as cdni
    , c.apellidos as capellido
    , group_concat(e.id_cliente ORDER BY e.id_cliente ASC SEPARATOR ' ')
    , group_concat(c.dni   SEPARATOR ' ')
  FROM reserva r 
  INNER JOIN cliente c on r.id_mainclient = c.id 
  INNER JOIN estancia e on r.id = e.id_reserva
  GROUP BY r.id
  ORDER BY rid DESC