The invention discloses a level-variable multi-level run-length limited modulation encoding method which comprises the following steps of: obtaining an ML-RLL (Multi-Level Run-Length-Limited) encoding code stream x with higher code rate R by using (M, d and k) encoding modes; combining or segmenting run lengths, changing the level M limitation of the specific run length or the d and k constraint conditions of the run lengths in the code stream x and obtaining a VML-RLL (Virtual Multi-Level Run-Length-Limited) code stream y with better channel characteristic. The invention reduces the intersymbol interference influence caused by the multi-level run length while farthest utilizing run-length redundancy. The readout characteristic of the level-variable multi-level run-length limited modulation encoding method is same with an ordinary run-length limited modulated DVD (Digital Versatile Disc), thus a servo control system of read data does not need to change. The signal recognition in the level-variable multi-level run-length limited modulation encoding method can be independently carried out in the two directions of the run length and the level. Under the condition of not changing laser wavelength and optical numerical aperture, the invention can markedly improve the storage capacity and the data transmission rate of a CD-ROM (Compact Disc Read-Only Memory) and keep good compatibility with a CD-ROM system at present.