實質課稅原則為租稅法之重要原則，本論文經由以下個案，探討稅捐稽徵機關以往對實質課稅原則之運用。 一、稅務稽徵機關以實質課稅為由否准四大金融業以債券前手息扣繳稅款抵繳其營利事業所得稅，何謂實質課稅原則?租稅法律主義與實質課稅原則應如何調和？ 二、從認購(售)權證成本之發生成因、課稅爭議之歷史沿革、並從徵納雙方對所得稅法之見解，探討實質課稅原則與租稅法律主義之競合。 三、複委託交易個案之探討－此處探討現行涉外所得課稅規定是否有不妥之處。 四、未來即將上市之海外來台第一上市股票、跨境ETF與新上市之指數型權證可能稅賦之探討－由相類似國內金融商品之課稅規定分析，探討稅負上是否具有一致性。 本研究建議： 一、稅捐稽徵機關應履行探究經濟實質之義務，方可主張實質課稅。 二、給付國外勞務報酬是否課稅應以實質認定，建議應定性為所得稅法第8條第9款之所得，並就在台固定營業場所或營業代理人之情形實質認定，以兼顧課稅要件明確與實質課稅精神。 三、應明文闡述支付國外券商複委託交易手續費屬營業稅課稅範圍之判定標準，以符合租稅法律主義之規範。 四、金融商品之課稅架構，應謹守租稅中立原則，保持一致性，避免對特定金融商品做特殊解釋。 / This research explored four cases in order to find out how the tax authority applies “substance versus form doctrine” in the some disputes. 1.The right to claim tax credit for withholding tax derived from bond interest had been long disputed. Can we say the tax authority’s view is "substance over form"? Did the amended Income Tax Act on 2007 solve the said dispute? 2.On the contrary, the tax authority isn’t in the view of "substance over form" for the tax deduction of hedge cost by warrant issuer. This study summary several Administrative Court adjudications to explore each party’s view. Can "substance over form" govern” “taxation by law“? 3.Securities firms conducting the business of accepting orders to trade foreign securities involve VAT and source income issues. This study addresses why the tax disputes arise and how to solve them. 4.This study also analyzes investors’ possible tax liability of coming List Securities by Foreign Issuers, Offshore ETF and newly Index Warrant. The suggestions in the above cases are as follows. 1.The tax authority should fulfill its duty to find out the economical substance then has a right disallow tax evasion. 2.The principles for determining Taiwan source income can adopt PE and business agent concept to mitigate the conflict between tax payers and tax authority. 3.The tax authority should interpret the criteria why offshore securities firms’ services should impose VAT. 4.The tax authority should be in the view of "substance over form" and maintain consistency while issuing tax ruling.