The process dissociation procedure (PDP) of implicit sequence learning states that the correct inclusion-task response contains the incorrect exclusion-task response. However, there has been no research to test the hypothesis. The current study used a single variable (Stimulus Onset Asynchrony SOA: 850 ms vs. 1350 ms) between-subjects design, with pre-task resting-state fMRI, to test and improve the classical PDP to the mutually exclusive theory (MET). (1) Behavioral data and neuroimaging data demonstrated that the classical PDP has not been validated. In the SOA = 850 ms group, the correct inclusion-task response was at chance, but the incorrect exclusion-task response occurred greater than chance. In the SOA = 850 ms group, the two responses were not correlated, but in the SOA = 1,350 ms group and putting the two groups together, the two responses were in contrast to each other. In each group, brain areas whose amplitude of low frequency fluctuations (ALFFs) in the resting-state related to the two responses were either completely different or opposite to one another. However, the results were perfectly consistent with the MET proposed by the present study which suggests that the correct inclusion-task response is equal to the correct exclusion-task response is equal to + , and the incorrect exclusion-task response is equal to . denotes the controlled response and and denote two different automatic responses. (2) The improved PDP was proposed to categorize the 12 kinds of triplets as delineating four knowledge types, namely non-acquisition of knowledge, uncontrollable knowledge, half-controllable knowledge, and controllable knowledge with the MET. ALFFs in the resting-state could predict the four knowledge types of the improved PDP among two groups. The participants' control of the four knowledge types (degree of consciousness) gradually improved. Correspondingly, the brain areas in the resting-state positively related to the four knowledge types, gradually changed from the sensory and motor network to the somatic sensorimotor network, and then to the implicit learning network, and then to the consciousness network. The brain areas in the resting-state negatively related to the four knowledge types gradually changed from the consciousness network to the sensory and motor network. As SOA increased, the brain areas associated with almost all the four knowledge types changed. (3) The inhomogeneous hypothesis of the MET is best suited to interpret behavioral and neuroimaging data; it states that the same components among the four knowledge types are not homogeneous, and the same knowledge types are not homogeneous between the two SOA groups.