Does chromosome cross occur over male and female or vice versa?
The question is unclear to me but hopefully that will help a little bit.


  My understanding is homologous chromosome pair, which means male and female chromosome


There is no male and female chromosome. Chromosomes have no sex. In humans, to the exception of chromosome Y all chromosome can be found in individuals of any sex.

There are paternally inherited chromosomes and maternally inherited chromosomes though. As you said the maternally inherited chromosome is indistinguishable from the paternally inherited chromosome when comparing their sequence (they may well differ in terms of epigenetic changes).


  chromosome inside the DNA.


A chromosome is not inside the DNA. DNA is the name of the very long molecule from which a chromosome is (mainly) made of. DNA can be organized in different forms one of which is into chromosomes (another one would be a plasmid for example). While it would still sound funny, it is more correct to talk about DNA inside a chromosome than talking about chromosome inside DNA.


  So if that's homologous how does male do with female?


This is very unclear...do what? Why would the paternally inherited chromosome (assuming this is what you mean by male chromosome) do anything with the maternally inherited chromosome rather than the other way around? While it is clear from the what follows that you would like to talk about recombination, I don't get where you're heading.


  does it flip over and change direction, that could not happen as male chromosome 1(say) is indistinguishable from female?


I don't get what kind of "flip" you are thinking about. You probably should have a look at the wikipedia article for cross-over.

In short, synapsis are formed during prophase I of meiosis and when segregation happen synapsis are resolved with a probability of $\frac{1}{2}$ of causing a recombination event. Synapsis occur as they allow matching pairs of homologous chromosomes together that will ensure their separation during anaphase 1. You should probably take some time to review the meaning of this paragraph.


  And what about the XY chromosome in male,say?


Sorry, that's a bit unclear too.


  I know some are pseudoautosomal, but most are normal sex chromosome nucleotides. So what about them?


Sounds like you misunderstand what a sex chromosome is and what pseudoautosomal mean.

In short, in humans, there is only one pair of sex chromosomes (XX or XY depending on the sex). The other 22 pairs of chromosomes are autosomes. There is no such thing as a pseudo-autosomal chromosome in humans but there is a pseudo-autosomal region on the Y-chromosome.

Most of the Y chromosome never recombine (while the X chromosome recombine in females only) as it is never present with another Y chromosome in the same cell. There is only a short sequence on top of the Y chromosome that recombines with the X chromosome, this region is called the pseudo-autosomal region. This region probably still exist to allow separation of X and Y chromosomes during anaphase I.



Please also note that you seem very focus on humans (without saying it and maybe without realizing it). The diversity of sex-determination is huge. You might want to have a look at Do males of all sexual species have Y chromosomes?