Resting-state functional MRI provides a viable tool for assessing brain dysfunctions in amyotrophic lateral sclerosis (ALS) without using explicit tasks. Altered resting brain functional connectivity (FC) in ALS has been reported in several studies but with large discrepancies in terms of the alteration directions. The purpose of this study was to provide new evidence for the resting FC disruptions in ALS. We focused on FC in the motor network as motor dysfunctions are a hallmark of ALS pathology. To test the hypothesis that ALS is associated with intermotor network FC changes, we compared FC of the key nodes of motor network between 12 ALS patients and 12 matched controls, and found both decreased and increased within-motor network FC in ALS patients. Increased FC between the bilateral superior parietal lobule and the right anterior inferior cerebellum was found to be correlated with disease severity, with higher FC related to more severe disease. The decreased motor network FC may be a result of motor function degradation in ALS, whereas the increased FC and its correlation to disease severity might suggest a brain mechanism to compensate the loss of the normal motor functionality in ALS. Our results also showed that the within-motor cortex FC except the within premotor area FC did not change in these early disease stage patients.