您正在where条件中使用左连接所涉及的列

where B.razonsocial <> ''

这是一个内部连接，请尝试将条件添加到相关的on子句中

select B.razonsocial as Empresa
    , Facturas
    , IFNULL(pay,0) as Pagos
    , (Facturas - IFNULL(pay,0)) Saldo 
    FROM (  
        select TblFacturasCompras.id_proveedor
            , TblProveedores.razonsocial
            , SUM(case when 
                        TblFacturasCompras.tipocomprobante = 'A' 
                        or TblFacturasCompras.tipocomprobante='B' 
                        or TblFacturasCompras.tipocomprobante = 'NDA' 
                        or TblFacturasCompras.tipocomprobante = 'NDB'  
                        or TblFacturasCompras.tipocomprobante = 'C'  
                        or TblFacturasCompras.tipocomprobante = 'NDC' 
                        or TblFacturasCompras.tipocomprobante = 'X' 
                    then TblFacturasCompras.total 
                    else -TblFacturasCompras.total end)  as Facturas 
        from TblFacturasCompras 
        left join TblProveedores on TblFacturasCompras.id_proveedor = TblProveedores.id 
        group by TblProveedores.id
    ) A 
    LEFT JOIN (
        select TblProveedores.id
            , TblProveedores.razonsocial
            , SUM(TblRecibosCompras.total) as Pay 
        from TblProveedores 
        left join TblRecibosCompras on TblRecibosCompras.id_proveedor = TblProveedores.id  
        group by TblProveedores.id
    ) B ON A.id_proveedor = B.id and  B.razonsocial <> '' 
    order by B.razonsocial Asc

还有一个建议，你可以用一个in子句而不是几个or子句

select B.razonsocial as Empresa
    , Facturas
    , IFNULL(pay,0) as Pagos
    , (Facturas - IFNULL(pay,0)) Saldo 
    FROM (  
        select TblFacturasCompras.id_proveedor
            , TblProveedores.razonsocial
            , SUM(case when 
                  TblFacturasCompras.tipocomprobante IN ('A','B','NDA','NDB','C','NDC','X') 
                    then TblFacturasCompras.total 
                    else -TblFacturasCompras.total end)  as Facturas 
        from TblFacturasCompras 
        left join TblProveedores on TblFacturasCompras.id_proveedor = TblProveedores.id 
        group by TblProveedores.id
    ) A 
    LEFT JOIN (
        select TblProveedores.id
            , TblProveedores.razonsocial
            , SUM(TblRecibosCompras.total) as Pay 
        from TblProveedores 
        left join TblRecibosCompras on TblRecibosCompras.id_proveedor = TblProveedores.id  
        group by TblProveedores.id
    ) B ON A.id_proveedor = B.id and  B.razonsocial <> '' 
    order by B.razonsocial Asc