Is the Pope limited in his authority over the Order of Malta? Is the Pope limited in his authority over the Catholic Order of Malta? How is the jurisdiction affected with the pope over the (Catholic) Sovereign Military Order of Malta since it is able to procure their own passports just like the Holy See is able to do so.


  Raymond de Souza: The Order of Malta is a sovereign entity, like any State, and the Holy Father has no authority to intervene in its internal administrative affairs, just as he may not intervene in the administration matters of Norway, India or the United States.


Is there anything in Canon Law that permits the pope to intervene in the affairs of the Sovereign Military Order of Malta?
Canon Law and secular law are separate concepts. According to New Advent:


  Contrasted with the imperial or Caesarian law (jus caesareum), canon law is sometimes styled pontifical law (jus pontificium), often also it is termed sacred law (jus sacrum), and sometimes even Divine law (jus divinum: c. 2, De privil.), as it concerns holy things, and has for its object the wellbeing of souls in the society divinely established by Jesus Christ. 


Source : "Canon Law", New Advent Catholic Encyclopedia

According to Canon 331 of the current Code of Canon Law on vatican.va:


  Can. 331 The bishop of the Roman Church, in whom continues the office given by the Lord uniquely to Peter, the first of the Apostles, and to be transmitted to his successors, is the head of the college of bishops, the Vicar of Christ, and the pastor of the universal Church on earth. By virtue of his office he possesses supreme, full, immediate, and universal ordinary power in the Church, which he is always able to exercise freely.


Source: Canon 331, Code of Canon Law

The jurisdiction being spoken of here is Ecclesiastical, not Civil. The Pope has the power to excommunicate officers of the Sovereign Military Order of Malta (SMOM), order them to do penance, grant special dispensations to them to have married priests, or otherwise exercise his ecclesiastical jurisdiction. The SMOM is sovereign from a civil sense - it is its own "Caesar" as much as the US is (or the Republic of Ireland, or Italy, or Poland, etc.).

Caesaropapism, where the Pope and Caesar are the same person, applied to the historical Papal States. It seems to apply today in the jurisdiction of the Vatican City state itself, but in no other place. With reference to the SMOM (or the USA, or Ireland, etc.), the Pope is the Pope and Caesar is the civil authorities.