There are six books in the Mortal Instruments series: City of Bones, City of Ashes, City of Glass, City of Fallen Angels, City of Lost Souls, and City of Heavenly Fire.
The Infernal Devices and the Mortal Instruments series alternated in their publication dates — one ID book, then one MI book, then one ID book, and so forth! Because the stories overlap and intertwine, it can be fun to read them in publication order — though if you choose not to, that will not affect your comprehension of either series. They complement each other, but each stands alone as a separate story.