The structural stability of the BEDT-TTF based organic crystals, which is considered to correlated with the anion structure sandwiching the BEDT-TTF layers, was investigated by scanning tunneling microscopy (STM). In the case of the (BEDT-TTF)₂XHg(SCN)₄(X=K, NH₄) crystal where the anion molecules have three-dimensional structure and are rigidly bonded each other, a perfectly arranged surface without any defects was observed over a wide range. In the case of β-(BEDT-TTF)₂I₃ crystal where the anion molecules are weakly bonded, on the contrary, a reconstructed surface with many defects was observed.