In this article, we study the Hitchin morphism over a smooth projective variety $X$. The Hitchin morphism is a map from the moduli space of Higgs bundles to the Hitchin base, which in general not surjective when the dimension of X is greater than one. Chen-Ng\^{o} introduced the spectral base, which is a closed subvariety of the Hitchin base. They conjectured that the Hitchin morphism is surjective to the spectral base and also proved that the surjectivity is equivalent to the existence of finite Cohen-Macaulayfications of the spectral varieties. For rank two Higgs bundles over a projective manifold $X$, we explicitly construct a finite Cohen-Macaulayfication of the spectral variety as a double branched covering of $X$, thereby confirming Chen-Ng\^{o}'s conjecture in this case. Moreover, using this Cohen-Macaulayfication, we can construct the Hitchin section for rank two Higgs bundles, which allows us to study the rigidity problem of the character variety and also to explore a generalization of the Milnor-Wood type inequality.