Linguists are not all of one mind when it comes to the exact meaning of morphophonemic, but I like the clarity of Michael Stubbs’ statement in his book Language and Literacy: The Sociolinguistics of Reading and Writing: “ . . . English spelling is not only phonemic; that is, it is not merely a system which relates sound units to letters. It is, rather, morphophonemic, relating orthographic units not only to phonemes, but also to morphemes, and therefore to grammatical and semantic units” (43). Phonemes are the smallest significant sounds of a language. Morphemes are its smallest parts that carry meaning. So a morphophonemic system like English spells not just sounds but also meanings.
Thus, certain meaningful English word parts are often spelled the same from word to word even though their pronunciations may differ. Consider, for instance, the noun plural suffix -s. In a word like cats the suffix is pronounced [s], [kats], while in a word like dogs it is pronounced [z], [dogz]. But in each word it is spelled <s>. Purely phonemic systems, such as the phonetic respellings in the preceding sentence, would have to use different spellings for the two sounds, <s> and <z>. The same thing is true of the past tense suffix -ed: In hugged it is pronounced [d]; in kissed, [t], and in cheated, [id], but in all three words it is spelled <ed>.
Another common and more complex example is the free base sign, which occurs in words like sign, resign, signal, designate: In sign and signal the letter <s> spells [s]; in resign and designate it spells [z]. In sign and resign the letter <i> spells a long vowel sound, in signal and designate it spells a short vowel sound. In sign and resign the letter <g> is silent; in signal and designate it spells the sound [g]. Again, a purely phonemic or phonetic system would have to have different spellings to distinguish all these different pronunciations, but because English is at least in part a morphophonemic system, and since the base sign is a constant semantic unit in all four words, it is spelled the same in all four, in spite of the more or less systematic changes in pronunciation. For other examples, consider the changes in the pronunciation of the <o>’s and <a>’s in photograph and photographer, or the changes in the pronunciation of <i> in sublime and sublimity.
The morphophonemic element in English spelling is one of the reasons that English spelling is often described as “confusing” and “chaotic” because it is not straightforwardly phonetic, or phonemic. However, one advantage of the morphophonemic approach is that it highlights simplifying unities in the language that would be obscured by a purely phonemic spelling system with all its different spellings of the same meaningful word parts.