The neurocognitive mechanism underlying negation processing remains controversial. While negation is suggested to modulate the access of word meaning, no such evidence has been observed in the event-related potential (ERP) literature on sentence processing. In the current study, we applied multivariate pattern analysis (MVPA) methods to examine the processing of sentence negation. We investigated two types of negative congruent/incongruent sentence pairs with truth-value evaluation (e.g., ‘A robin is a/not a bird’) and without (e.g., ‘The woman reads a/no book’). At the target word, ERP results showed consistent N400 effects for semantic congruency, whose amplitudes remain unmodulated across both sentence types and polarity conditions. With MVPA, however, for negative vs. positive sentences, decoding across time analysis showed decreased decoding accuracy for semantic congruency within the N400 window. In addition, temporal generalization revealed serial bi-phasic N400-P600 patterns for semantic congruency across sentence types and polarity. Further, with the cross-decoding approach, we showed that the cognitive processes underlying the N400 window for both affirmative and negative sentences are comparable; whereas in the P600 window, negative sentences showed a distinct pattern from their affirmative counterparts. Our results from MVPA—but not the ERPs—thus speak for a more interactive, but nevertheless serial and bi-phasic processing account of negation processing. We also discuss the advantage of applying MVPA in addition to the classical univariate methods for a better understanding of the neurobiology of negation processing and language comprehension alike.